Starting phenix.real_space_refine on Mon Dec 30 12:13:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rw6_24709/12_2024/7rw6_24709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rw6_24709/12_2024/7rw6_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_24709/12_2024/7rw6_24709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rw6_24709/12_2024/7rw6_24709.map" model { file = "/net/cci-nas-00/data/ceres_data/7rw6_24709/12_2024/7rw6_24709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rw6_24709/12_2024/7rw6_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-5532/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: 7.99, per 1000 atoms: 0.61 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: 2.95 Conformation dependent library (CDL) restraints added in 1.7 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: 1.56 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: 3.92 Time building geometry restraints manager: 3.46 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: 0.00 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: 2.190 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.080 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.200 ------------------------------------------------------------------------------- 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 : 0.003 0.033 13458 Z= 0.185 Angle : 0.550 11.682 18234 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 *********************** 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 : 1.586 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: 1.3623 time to fit residues: 387.7669 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 : 1.388 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.5980 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: 0.9582 ------------------------------------------------------------------------------- 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 ** 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 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13458 Z= 0.291 Angle : 0.611 9.360 18234 Z= 0.319 Chirality : 0.044 0.149 1950 Planarity : 0.005 0.074 2360 Dihedral : 4.929 82.533 1814 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.65 % Allowed : 7.89 % Favored : 90.46 % 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: 0.86 (0.19), residues: 800 sheet: -0.64 (0.39), residues: 166 loop : -0.56 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 277 HIS 0.005 0.001 HIS C 9 PHE 0.020 0.002 PHE A 520 TYR 0.015 0.002 TYR C 716 ARG 0.010 0.001 ARG C 704 *********************** 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 266 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7294 (tp30) cc_final: 0.6743 (tp30) REVERT: A 68 MET cc_start: 0.7757 (ptt) cc_final: 0.6846 (ptt) REVERT: B 231 MET cc_start: 0.6690 (pmm) cc_final: 0.6485 (pmm) REVERT: C 88 ARG cc_start: 0.7981 (ttt-90) cc_final: 0.7779 (ttp80) REVERT: C 379 GLN cc_start: 0.8414 (tp-100) cc_final: 0.7953 (tp-100) REVERT: C 674 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7367 (tp30) outliers start: 23 outliers final: 12 residues processed: 253 average time/residue: 1.3015 time to fit residues: 359.6559 Evaluate side-chains 249 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 C residue 305 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13458 Z= 0.256 Angle : 0.596 9.857 18234 Z= 0.308 Chirality : 0.043 0.153 1950 Planarity : 0.005 0.052 2360 Dihedral : 4.964 85.721 1814 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.51 % Allowed : 9.97 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.19), residues: 784 sheet: -0.83 (0.38), residues: 166 loop : -0.62 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 277 HIS 0.004 0.001 HIS A 558 PHE 0.019 0.001 PHE A 520 TYR 0.016 0.002 TYR A 322 ARG 0.006 0.000 ARG D 351 *********************** 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 279 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7302 (tp30) cc_final: 0.6773 (tp30) REVERT: A 68 MET cc_start: 0.7818 (ptt) cc_final: 0.7016 (ptt) REVERT: A 338 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8532 (mtpt) REVERT: B 231 MET cc_start: 0.6681 (pmm) cc_final: 0.6450 (pmm) REVERT: B 332 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7952 (pp30) REVERT: C 54 GLU cc_start: 0.8311 (tp30) cc_final: 0.8068 (tm-30) REVERT: C 215 ARG cc_start: 0.7775 (ptp-170) cc_final: 0.7571 (ttm110) REVERT: C 674 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7401 (tp30) REVERT: D 229 VAL cc_start: 0.8642 (t) cc_final: 0.8198 (m) REVERT: D 339 ASP cc_start: 0.7702 (p0) cc_final: 0.7322 (p0) outliers start: 35 outliers final: 11 residues processed: 260 average time/residue: 1.3197 time to fit residues: 375.1357 Evaluate side-chains 246 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 D residue 212 ARG Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 140 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 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 689 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13458 Z= 0.256 Angle : 0.607 9.494 18234 Z= 0.313 Chirality : 0.043 0.146 1950 Planarity : 0.005 0.084 2360 Dihedral : 5.059 92.517 1814 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.30 % Allowed : 11.98 % Favored : 85.72 % 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: 0.98 (0.19), residues: 786 sheet: -0.94 (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 557 HIS 0.004 0.001 HIS A 558 PHE 0.019 0.001 PHE A 520 TYR 0.016 0.002 TYR C 322 ARG 0.012 0.000 ARG C 704 *********************** 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 270 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7323 (tp30) cc_final: 0.6794 (tp30) REVERT: A 68 MET cc_start: 0.7842 (ptt) cc_final: 0.7019 (ptt) REVERT: A 82 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: A 338 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8532 (mtpt) REVERT: B 231 MET cc_start: 0.6675 (pmm) cc_final: 0.6437 (pmm) REVERT: C 593 MET cc_start: 0.7063 (tpt) cc_final: 0.6672 (tpt) REVERT: C 674 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7372 (tp30) REVERT: D 339 ASP cc_start: 0.7755 (p0) cc_final: 0.7504 (p0) REVERT: D 340 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7671 (mp0) outliers start: 32 outliers final: 11 residues processed: 250 average time/residue: 1.2589 time to fit residues: 343.8623 Evaluate side-chains 244 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 230 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU 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 334 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain C residue 43 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 340 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.0010 chunk 88 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13458 Z= 0.199 Angle : 0.589 9.685 18234 Z= 0.302 Chirality : 0.042 0.145 1950 Planarity : 0.004 0.049 2360 Dihedral : 4.570 31.162 1814 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.51 % Allowed : 12.70 % Favored : 84.79 % 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: 0.20 (0.21), residues: 1606 helix: 1.08 (0.19), residues: 784 sheet: -1.05 (0.38), residues: 166 loop : -0.61 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.003 0.001 HIS A 264 PHE 0.018 0.001 PHE A 270 TYR 0.018 0.001 TYR C 322 ARG 0.009 0.000 ARG C 215 *********************** 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 276 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: A 338 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8522 (mtpt) REVERT: A 606 ASP cc_start: 0.8227 (t70) cc_final: 0.7879 (t70) REVERT: C 54 GLU cc_start: 0.8276 (tp30) cc_final: 0.7983 (tp30) REVERT: C 87 GLU cc_start: 0.8249 (tp30) cc_final: 0.7964 (mm-30) REVERT: C 593 MET cc_start: 0.6961 (tpt) cc_final: 0.6633 (tpt) REVERT: C 674 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7350 (tp30) REVERT: D 229 VAL cc_start: 0.8727 (t) cc_final: 0.8253 (m) REVERT: D 340 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7751 (mp0) outliers start: 35 outliers final: 9 residues processed: 258 average time/residue: 1.3206 time to fit residues: 371.8798 Evaluate side-chains 249 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU 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 C residue 95 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 340 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13458 Z= 0.204 Angle : 0.588 10.013 18234 Z= 0.300 Chirality : 0.042 0.146 1950 Planarity : 0.004 0.050 2360 Dihedral : 4.446 19.017 1812 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.79 % Allowed : 14.20 % Favored : 84.00 % 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: 0.20 (0.21), residues: 1606 helix: 1.12 (0.19), residues: 784 sheet: -1.12 (0.38), residues: 166 loop : -0.66 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 287 HIS 0.004 0.001 HIS A 264 PHE 0.026 0.001 PHE A 270 TYR 0.017 0.001 TYR C 322 ARG 0.006 0.000 ARG D 351 *********************** 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 265 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7341 (tp30) cc_final: 0.6701 (tp30) REVERT: A 82 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7385 (mp10) REVERT: A 215 ARG cc_start: 0.7673 (ptp90) cc_final: 0.7258 (ttm110) REVERT: A 324 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6789 (tm-30) REVERT: A 328 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7578 (mtm110) REVERT: A 338 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8524 (mtpt) REVERT: A 606 ASP cc_start: 0.8242 (t70) cc_final: 0.7885 (t70) REVERT: B 229 VAL cc_start: 0.8857 (t) cc_final: 0.8424 (m) REVERT: B 231 MET cc_start: 0.6986 (pmm) cc_final: 0.6758 (pmm) REVERT: C 54 GLU cc_start: 0.8319 (tp30) cc_final: 0.8053 (tm-30) REVERT: C 82 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: C 87 GLU cc_start: 0.8241 (tp30) cc_final: 0.7996 (tm-30) REVERT: C 272 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: C 311 ASP cc_start: 0.8085 (p0) cc_final: 0.7674 (p0) REVERT: C 593 MET cc_start: 0.7005 (tpt) cc_final: 0.6647 (tpt) REVERT: C 674 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7345 (tp30) REVERT: D 229 VAL cc_start: 0.8739 (t) cc_final: 0.8259 (m) REVERT: D 340 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7797 (mp0) outliers start: 25 outliers final: 10 residues processed: 251 average time/residue: 1.2903 time to fit residues: 353.8039 Evaluate side-chains 252 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU 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 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 D residue 212 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 340 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13458 Z= 0.268 Angle : 0.611 10.285 18234 Z= 0.312 Chirality : 0.043 0.147 1950 Planarity : 0.005 0.103 2360 Dihedral : 4.521 18.807 1812 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.08 % Allowed : 14.85 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1606 helix: 1.14 (0.19), residues: 772 sheet: -1.16 (0.38), residues: 166 loop : -0.68 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 C 322 ARG 0.023 0.001 ARG C 704 *********************** 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 265 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 1.541 Fit side-chains REVERT: A 64 GLU cc_start: 0.7403 (tp30) cc_final: 0.6755 (tp30) REVERT: A 82 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: A 215 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7296 (ttm110) REVERT: A 260 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8432 (ttp) REVERT: A 328 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7579 (mtm110) REVERT: A 338 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8553 (mtpt) REVERT: A 606 ASP cc_start: 0.8229 (t70) cc_final: 0.7902 (t70) REVERT: B 229 VAL cc_start: 0.8873 (t) cc_final: 0.8430 (m) REVERT: B 231 MET cc_start: 0.6911 (pmm) cc_final: 0.6668 (pmm) REVERT: C 54 GLU cc_start: 0.8339 (tp30) cc_final: 0.8055 (tp30) REVERT: C 64 GLU cc_start: 0.7345 (tp30) cc_final: 0.6512 (tp30) REVERT: C 82 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7764 (mp10) REVERT: C 87 GLU cc_start: 0.8257 (tp30) cc_final: 0.8006 (tm-30) REVERT: C 272 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: C 311 ASP cc_start: 0.8087 (p0) cc_final: 0.7673 (p0) REVERT: C 593 MET cc_start: 0.7163 (tpt) cc_final: 0.6881 (tpt) REVERT: C 600 GLN cc_start: 0.8104 (mt0) cc_final: 0.7770 (mp10) REVERT: C 674 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7358 (tp30) REVERT: D 229 VAL cc_start: 0.8771 (t) cc_final: 0.8302 (m) outliers start: 29 outliers final: 16 residues processed: 245 average time/residue: 1.3821 time to fit residues: 369.4259 Evaluate side-chains 264 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU 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 260 MET 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 259 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 367 GLN 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 D residue 212 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13458 Z= 0.223 Angle : 0.599 10.280 18234 Z= 0.307 Chirality : 0.043 0.147 1950 Planarity : 0.004 0.058 2360 Dihedral : 4.483 18.872 1812 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.79 % Allowed : 15.93 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1606 helix: 1.10 (0.19), residues: 784 sheet: -1.22 (0.38), residues: 166 loop : -0.69 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 287 HIS 0.004 0.001 HIS A 264 PHE 0.023 0.001 PHE A 270 TYR 0.017 0.001 TYR C 322 ARG 0.012 0.000 ARG C 704 *********************** 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: 25 poor density : 235 time to evaluate : 1.626 Fit side-chains REVERT: A 64 GLU cc_start: 0.7393 (tp30) cc_final: 0.6745 (tp30) REVERT: A 82 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: A 215 ARG cc_start: 0.7683 (ptp90) cc_final: 0.7288 (ttm110) REVERT: A 260 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8345 (ttp) REVERT: A 328 ARG cc_start: 0.7920 (ttm110) cc_final: 0.7593 (mtm110) REVERT: A 338 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8453 (mtpt) REVERT: A 606 ASP cc_start: 0.8217 (t70) cc_final: 0.7852 (t70) REVERT: B 229 VAL cc_start: 0.8881 (t) cc_final: 0.8459 (m) REVERT: B 231 MET cc_start: 0.6921 (pmm) cc_final: 0.6711 (pmm) REVERT: C 64 GLU cc_start: 0.7339 (tp30) cc_final: 0.6506 (tp30) REVERT: C 76 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7598 (mtm-85) REVERT: C 82 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: C 87 GLU cc_start: 0.8244 (tp30) cc_final: 0.8011 (tm-30) REVERT: C 272 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: C 311 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7630 (p0) REVERT: C 593 MET cc_start: 0.7154 (tpt) cc_final: 0.6862 (tpt) REVERT: D 229 VAL cc_start: 0.8769 (t) cc_final: 0.8263 (m) outliers start: 25 outliers final: 10 residues processed: 247 average time/residue: 1.3213 time to fit residues: 357.8634 Evaluate side-chains 244 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 262 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 131 optimal weight: 0.4980 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13458 Z= 0.247 Angle : 0.622 10.701 18234 Z= 0.318 Chirality : 0.043 0.146 1950 Planarity : 0.005 0.054 2360 Dihedral : 4.509 19.047 1812 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.15 % Allowed : 16.14 % Favored : 81.71 % 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: 0.16 (0.21), residues: 1606 helix: 1.14 (0.19), residues: 774 sheet: -1.25 (0.38), residues: 166 loop : -0.69 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 287 HIS 0.004 0.001 HIS A 264 PHE 0.018 0.001 PHE C 270 TYR 0.025 0.002 TYR C 612 ARG 0.011 0.000 ARG C 704 *********************** 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 254 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 1.483 Fit side-chains REVERT: A 64 GLU cc_start: 0.7422 (tp30) cc_final: 0.6769 (tp30) REVERT: A 82 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: A 215 ARG cc_start: 0.7692 (ptp90) cc_final: 0.7297 (ttm110) REVERT: A 260 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8370 (ttp) REVERT: A 328 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7587 (mtm110) REVERT: A 606 ASP cc_start: 0.8266 (t70) cc_final: 0.7910 (t70) REVERT: B 229 VAL cc_start: 0.8890 (t) cc_final: 0.8458 (m) REVERT: B 231 MET cc_start: 0.6970 (pmm) cc_final: 0.6759 (pmm) REVERT: C 64 GLU cc_start: 0.7364 (tp30) cc_final: 0.6537 (tp30) REVERT: C 76 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7549 (mtm-85) REVERT: C 82 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: C 87 GLU cc_start: 0.8246 (tp30) cc_final: 0.8028 (tm-30) REVERT: C 272 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: C 311 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7725 (p0) REVERT: C 593 MET cc_start: 0.7168 (tpt) cc_final: 0.6864 (tpt) REVERT: D 229 VAL cc_start: 0.8726 (t) cc_final: 0.8220 (m) outliers start: 30 outliers final: 14 residues processed: 243 average time/residue: 1.3171 time to fit residues: 349.2429 Evaluate side-chains 247 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 260 MET 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 366 SER Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain C residue 76 ARG 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 311 ASP Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13458 Z= 0.264 Angle : 0.637 11.051 18234 Z= 0.327 Chirality : 0.044 0.154 1950 Planarity : 0.005 0.050 2360 Dihedral : 4.547 19.105 1812 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.51 % Allowed : 16.93 % Favored : 81.56 % 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: 1.14 (0.19), residues: 772 sheet: -1.25 (0.38), residues: 166 loop : -0.73 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 287 HIS 0.005 0.001 HIS A 264 PHE 0.023 0.001 PHE A 270 TYR 0.023 0.002 TYR C 612 ARG 0.009 0.000 ARG A 99 ********************** 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 250 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 1.594 Fit side-chains REVERT: A 64 GLU cc_start: 0.7452 (tp30) cc_final: 0.6796 (tp30) REVERT: A 82 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: A 260 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8357 (ttp) REVERT: A 328 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7551 (mtm110) REVERT: B 229 VAL cc_start: 0.8938 (t) cc_final: 0.8559 (m) REVERT: B 231 MET cc_start: 0.6942 (pmm) cc_final: 0.6721 (pmm) REVERT: C 64 GLU cc_start: 0.7389 (tp30) cc_final: 0.6558 (tp30) REVERT: C 76 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7537 (mtm-85) REVERT: C 82 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: C 272 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: C 311 ASP cc_start: 0.8072 (p0) cc_final: 0.7763 (p0) REVERT: D 229 VAL cc_start: 0.8695 (t) cc_final: 0.8170 (m) REVERT: D 231 MET cc_start: 0.6838 (pmm) cc_final: 0.5846 (pmm) outliers start: 21 outliers final: 15 residues processed: 241 average time/residue: 1.3015 time to fit residues: 343.0369 Evaluate side-chains 244 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 322 TYR 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 366 SER Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain C residue 76 ARG 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 D residue 212 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0770 chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 128 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 132 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3756 r_free = 0.3756 target = 0.111538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095743 restraints weight = 22489.996| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.17 r_work: 0.3369 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13458 Z= 0.192 Angle : 0.636 11.277 18234 Z= 0.322 Chirality : 0.042 0.146 1950 Planarity : 0.005 0.049 2360 Dihedral : 4.481 19.014 1812 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.58 % Allowed : 17.50 % Favored : 80.92 % 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: 0.12 (0.21), residues: 1606 helix: 1.12 (0.19), residues: 784 sheet: -1.30 (0.38), residues: 166 loop : -0.74 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 287 HIS 0.004 0.001 HIS A 264 PHE 0.019 0.001 PHE A 270 TYR 0.023 0.001 TYR C 612 ARG 0.009 0.000 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5968.42 seconds wall clock time: 107 minutes 48.97 seconds (6468.97 seconds total)