Starting phenix.real_space_refine on Wed Feb 4 20:43:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rw6_24709/02_2026/7rw6_24709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rw6_24709/02_2026/7rw6_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rw6_24709/02_2026/7rw6_24709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rw6_24709/02_2026/7rw6_24709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rw6_24709/02_2026/7rw6_24709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rw6_24709/02_2026/7rw6_24709.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 3.34, per 1000 atoms: 0.25 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: 1.15 Conformation dependent library (CDL) restraints added in 726.8 milliseconds 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: 0.62 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: 2.39 Time building geometry restraints manager: 1.59 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- 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 : 9.23 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (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 ARG 0.003 0.000 ARG A 328 TYR 0.018 0.001 TYR C 61 PHE 0.014 0.001 PHE C 542 TRP 0.011 0.001 TRP A 554 HIS 0.003 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00282 (13458) covalent geometry : angle 0.54967 (18234) SS BOND : bond 0.00348 ( 2) SS BOND : angle 2.02063 ( 4) hydrogen bonds : bond 0.17479 ( 600) hydrogen bonds : angle 6.39832 ( 1767) metal coordination : bond 0.27952 ( 6) *********************** 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 : 0.515 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: 0.6725 time to fit residues: 190.8766 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 : 0.531 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.097087 restraints weight = 22550.378| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.16 r_work: 0.3392 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13466 Z= 0.142 Angle : 0.586 9.472 18238 Z= 0.306 Chirality : 0.043 0.146 1950 Planarity : 0.005 0.071 2360 Dihedral : 4.841 85.248 1814 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1606 helix: 1.16 (0.19), residues: 762 sheet: -0.63 (0.39), residues: 166 loop : -0.47 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 704 TYR 0.014 0.001 TYR C 716 PHE 0.015 0.001 PHE C 520 TRP 0.011 0.001 TRP D 277 HIS 0.005 0.001 HIS C 9 Details of bonding type rmsd covalent geometry : bond 0.00309 (13458) covalent geometry : angle 0.58579 (18234) SS BOND : bond 0.00532 ( 2) SS BOND : angle 1.92524 ( 4) hydrogen bonds : bond 0.04651 ( 600) hydrogen bonds : angle 4.92231 ( 1767) metal coordination : bond 0.00434 ( 6) *********************** 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 264 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7677 (tp30) cc_final: 0.7083 (tp30) REVERT: A 68 MET cc_start: 0.7752 (ptt) cc_final: 0.7020 (ptt) REVERT: A 662 TYR cc_start: 0.7530 (m-10) cc_final: 0.7285 (m-10) REVERT: B 231 MET cc_start: 0.6988 (pmm) cc_final: 0.6653 (pmm) REVERT: C 674 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7649 (tp30) REVERT: D 332 GLN cc_start: 0.8298 (pp30) cc_final: 0.7981 (pp30) outliers start: 22 outliers final: 9 residues processed: 251 average time/residue: 0.6110 time to fit residues: 167.3463 Evaluate side-chains 239 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 30 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 148 optimal weight: 0.0770 chunk 60 optimal weight: 0.5980 chunk 79 optimal weight: 0.0870 chunk 144 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096152 restraints weight = 22778.444| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.14 r_work: 0.3376 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1456 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= 0.134 Angle : 0.568 8.610 18238 Z= 0.294 Chirality : 0.042 0.147 1950 Planarity : 0.004 0.049 2360 Dihedral : 4.820 85.905 1814 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.30 % Allowed : 9.83 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1606 helix: 1.17 (0.19), residues: 772 sheet: -0.86 (0.38), residues: 166 loop : -0.46 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 304 TYR 0.016 0.001 TYR B 319 PHE 0.016 0.001 PHE C 520 TRP 0.010 0.001 TRP A 554 HIS 0.004 0.001 HIS C 9 Details of bonding type rmsd covalent geometry : bond 0.00297 (13458) covalent geometry : angle 0.56785 (18234) SS BOND : bond 0.00514 ( 2) SS BOND : angle 1.73280 ( 4) hydrogen bonds : bond 0.04223 ( 600) hydrogen bonds : angle 4.70718 ( 1767) metal coordination : bond 0.00278 ( 6) *********************** 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 276 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 ASP cc_start: 0.8354 (t70) cc_final: 0.7994 (t70) REVERT: A 662 TYR cc_start: 0.7452 (m-10) cc_final: 0.7251 (m-10) REVERT: B 231 MET cc_start: 0.6982 (pmm) cc_final: 0.6667 (pmm) REVERT: B 332 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7979 (pp30) REVERT: C 54 GLU cc_start: 0.8604 (tp30) cc_final: 0.8388 (tm-30) REVERT: C 215 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7563 (ttm110) REVERT: C 674 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7701 (tp30) REVERT: D 235 MET cc_start: 0.6871 (tmm) cc_final: 0.6661 (tmm) REVERT: D 292 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7421 (mt-10) outliers start: 32 outliers final: 13 residues processed: 258 average time/residue: 0.6272 time to fit residues: 176.4149 Evaluate side-chains 251 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 265 SER 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 332 GLN 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 D residue 212 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 292 GLU 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 81 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095732 restraints weight = 22654.371| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.14 r_work: 0.3379 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13466 Z= 0.146 Angle : 0.585 10.295 18238 Z= 0.300 Chirality : 0.042 0.145 1950 Planarity : 0.004 0.049 2360 Dihedral : 4.418 29.678 1814 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.94 % Allowed : 12.12 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1606 helix: 1.20 (0.19), residues: 772 sheet: -0.91 (0.38), residues: 166 loop : -0.50 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 328 TYR 0.016 0.001 TYR B 319 PHE 0.023 0.001 PHE A 270 TRP 0.010 0.001 TRP A 557 HIS 0.004 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00331 (13458) covalent geometry : angle 0.58382 (18234) SS BOND : bond 0.00636 ( 2) SS BOND : angle 2.02874 ( 4) hydrogen bonds : bond 0.04115 ( 600) hydrogen bonds : angle 4.60137 ( 1767) metal coordination : bond 0.00308 ( 6) *********************** 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: 27 poor density : 241 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7814 (tp30) cc_final: 0.7130 (tp30) REVERT: A 82 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: A 494 GLN cc_start: 0.8560 (pt0) cc_final: 0.8310 (pt0) REVERT: B 231 MET cc_start: 0.6971 (pmm) cc_final: 0.6637 (pmm) REVERT: C 215 ARG cc_start: 0.7822 (ptp-170) cc_final: 0.7515 (ttm110) REVERT: C 593 MET cc_start: 0.6996 (tpt) cc_final: 0.6647 (tpt) REVERT: C 674 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7721 (tp30) outliers start: 27 outliers final: 11 residues processed: 253 average time/residue: 0.6092 time to fit residues: 167.9790 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 : 0.500 ------------------------------------------------------------------------------- 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 726 TYR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 305 SER 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 339 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095423 restraints weight = 22866.552| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.17 r_work: 0.3379 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1715 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= 0.139 Angle : 0.585 10.884 18238 Z= 0.300 Chirality : 0.042 0.147 1950 Planarity : 0.004 0.049 2360 Dihedral : 4.350 19.132 1812 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.01 % Allowed : 13.41 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1606 helix: 1.22 (0.19), residues: 772 sheet: -0.97 (0.38), residues: 166 loop : -0.55 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.017 0.001 TYR B 319 PHE 0.029 0.001 PHE C 270 TRP 0.009 0.001 TRP A 557 HIS 0.003 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00314 (13458) covalent geometry : angle 0.58409 (18234) SS BOND : bond 0.00829 ( 2) SS BOND : angle 2.53202 ( 4) hydrogen bonds : bond 0.04004 ( 600) hydrogen bonds : angle 4.54061 ( 1767) metal coordination : bond 0.00266 ( 6) *********************** 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 272 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7859 (tp30) cc_final: 0.7129 (tp30) REVERT: A 82 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: A 215 ARG cc_start: 0.7619 (ptp90) cc_final: 0.7149 (ttm110) REVERT: A 606 ASP cc_start: 0.8416 (t70) cc_final: 0.8051 (t70) REVERT: B 229 VAL cc_start: 0.8732 (t) cc_final: 0.8329 (m) REVERT: B 231 MET cc_start: 0.6995 (pmm) cc_final: 0.6626 (pmm) REVERT: C 54 GLU cc_start: 0.8562 (tp30) cc_final: 0.8317 (tp30) REVERT: C 87 GLU cc_start: 0.8435 (tp30) cc_final: 0.8221 (mm-30) REVERT: C 215 ARG cc_start: 0.7831 (ptp-170) cc_final: 0.7523 (ttm110) REVERT: C 593 MET cc_start: 0.6966 (tpt) cc_final: 0.6580 (tpt) REVERT: C 674 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7689 (tp30) REVERT: D 339 ASP cc_start: 0.8123 (p0) cc_final: 0.7776 (p0) REVERT: D 340 GLU cc_start: 0.8090 (mp0) cc_final: 0.7411 (mp0) outliers start: 28 outliers final: 11 residues processed: 255 average time/residue: 0.5473 time to fit residues: 152.8762 Evaluate side-chains 257 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 245 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 726 TYR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 322 TYR 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 337 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 494 GLN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.110055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094170 restraints weight = 22571.069| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.15 r_work: 0.3346 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 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 = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1825 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= 0.169 Angle : 0.602 10.921 18238 Z= 0.308 Chirality : 0.043 0.142 1950 Planarity : 0.005 0.091 2360 Dihedral : 4.445 19.062 1812 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.22 % Allowed : 13.63 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1606 helix: 1.18 (0.19), residues: 772 sheet: -1.05 (0.38), residues: 166 loop : -0.63 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 704 TYR 0.019 0.002 TYR B 319 PHE 0.022 0.001 PHE C 270 TRP 0.010 0.001 TRP A 263 HIS 0.004 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00390 (13458) covalent geometry : angle 0.60034 (18234) SS BOND : bond 0.01358 ( 2) SS BOND : angle 3.24485 ( 4) hydrogen bonds : bond 0.04117 ( 600) hydrogen bonds : angle 4.53840 ( 1767) metal coordination : bond 0.00401 ( 6) *********************** 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 282 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7909 (tp30) cc_final: 0.7153 (tp30) REVERT: A 82 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: A 606 ASP cc_start: 0.8334 (t70) cc_final: 0.8001 (t70) REVERT: B 229 VAL cc_start: 0.8765 (t) cc_final: 0.8364 (m) REVERT: B 231 MET cc_start: 0.6911 (pmm) cc_final: 0.6545 (pmm) REVERT: B 268 ASP cc_start: 0.8277 (t0) cc_final: 0.8050 (t0) REVERT: C 54 GLU cc_start: 0.8600 (tp30) cc_final: 0.8342 (tp30) REVERT: C 87 GLU cc_start: 0.8445 (tp30) cc_final: 0.8153 (tm-30) REVERT: C 215 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7569 (ttm110) REVERT: C 311 ASP cc_start: 0.8268 (p0) cc_final: 0.7817 (p0) REVERT: C 593 MET cc_start: 0.7007 (tpt) cc_final: 0.6689 (tpt) REVERT: C 674 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7696 (tp30) outliers start: 31 outliers final: 17 residues processed: 264 average time/residue: 0.5333 time to fit residues: 154.2084 Evaluate side-chains 265 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 265 SER 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 95 LEU Chi-restraints excluded: chain C residue 305 SER 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 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 51 optimal weight: 0.0670 chunk 105 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 82 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN C 494 GLN ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096399 restraints weight = 22546.635| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.16 r_work: 0.3396 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13466 Z= 0.121 Angle : 0.581 10.640 18238 Z= 0.297 Chirality : 0.041 0.143 1950 Planarity : 0.004 0.048 2360 Dihedral : 4.350 18.296 1812 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.72 % Allowed : 14.85 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1606 helix: 1.15 (0.19), residues: 784 sheet: -1.15 (0.38), residues: 166 loop : -0.65 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 704 TYR 0.019 0.001 TYR B 319 PHE 0.019 0.001 PHE C 270 TRP 0.013 0.001 TRP D 287 HIS 0.003 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00266 (13458) covalent geometry : angle 0.58041 (18234) SS BOND : bond 0.00723 ( 2) SS BOND : angle 1.97089 ( 4) hydrogen bonds : bond 0.03724 ( 600) hydrogen bonds : angle 4.51157 ( 1767) metal coordination : bond 0.00191 ( 6) *********************** 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: 24 poor density : 241 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7777 (tp30) cc_final: 0.7053 (tp30) REVERT: A 82 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: A 215 ARG cc_start: 0.7620 (ptp90) cc_final: 0.7167 (ttm110) REVERT: A 606 ASP cc_start: 0.8260 (t70) cc_final: 0.7944 (t70) REVERT: B 229 VAL cc_start: 0.8787 (t) cc_final: 0.8390 (m) REVERT: B 231 MET cc_start: 0.6953 (pmm) cc_final: 0.6582 (pmm) REVERT: B 363 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: C 54 GLU cc_start: 0.8594 (tp30) cc_final: 0.8324 (tp30) REVERT: C 82 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: C 215 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7519 (ttm110) REVERT: C 311 ASP cc_start: 0.8208 (p0) cc_final: 0.7774 (p0) REVERT: C 593 MET cc_start: 0.6967 (tpt) cc_final: 0.6651 (tpt) REVERT: C 674 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7652 (tp30) outliers start: 24 outliers final: 11 residues processed: 250 average time/residue: 0.5858 time to fit residues: 160.5587 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 : 0.516 ------------------------------------------------------------------------------- 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 680 SER Chi-restraints excluded: chain A residue 726 TYR 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 322 TYR 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 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 118 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** 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 = 0.3754 r_free = 0.3754 target = 0.111781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096044 restraints weight = 22341.504| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.16 r_work: 0.3378 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13466 Z= 0.143 Angle : 0.598 10.342 18238 Z= 0.304 Chirality : 0.042 0.147 1950 Planarity : 0.004 0.053 2360 Dihedral : 4.376 17.972 1812 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.51 % Allowed : 15.93 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1606 helix: 1.16 (0.19), residues: 784 sheet: -1.14 (0.38), residues: 166 loop : -0.66 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 328 TYR 0.024 0.002 TYR C 612 PHE 0.017 0.001 PHE A 520 TRP 0.013 0.001 TRP B 287 HIS 0.006 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00327 (13458) covalent geometry : angle 0.59774 (18234) SS BOND : bond 0.00931 ( 2) SS BOND : angle 1.94766 ( 4) hydrogen bonds : bond 0.03871 ( 600) hydrogen bonds : angle 4.48031 ( 1767) metal coordination : bond 0.00290 ( 6) *********************** 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 254 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7853 (tp30) cc_final: 0.7100 (tp30) REVERT: A 82 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: A 215 ARG cc_start: 0.7662 (ptp90) cc_final: 0.7210 (ttm110) REVERT: A 270 PHE cc_start: 0.8563 (t80) cc_final: 0.8307 (t80) REVERT: A 606 ASP cc_start: 0.8360 (t70) cc_final: 0.8060 (t70) REVERT: B 229 VAL cc_start: 0.8807 (t) cc_final: 0.8421 (m) REVERT: B 231 MET cc_start: 0.6931 (pmm) cc_final: 0.6530 (pmm) REVERT: B 363 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: C 54 GLU cc_start: 0.8589 (tp30) cc_final: 0.8339 (tp30) REVERT: C 64 GLU cc_start: 0.7753 (tp30) cc_final: 0.6894 (tp30) REVERT: C 82 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: C 215 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7520 (ttm110) REVERT: C 311 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7720 (p0) REVERT: C 317 ASP cc_start: 0.8026 (m-30) cc_final: 0.7822 (m-30) REVERT: C 593 MET cc_start: 0.7050 (tpt) cc_final: 0.6825 (tpt) REVERT: D 229 VAL cc_start: 0.8664 (t) cc_final: 0.8071 (m) outliers start: 21 outliers final: 10 residues processed: 241 average time/residue: 0.6405 time to fit residues: 169.0523 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 : 0.550 ------------------------------------------------------------------------------- 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 265 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain B residue 363 GLU 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 311 ASP Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 102 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 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 384 ASN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN 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 = 0.3746 r_free = 0.3746 target = 0.111363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.095716 restraints weight = 22599.445| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.15 r_work: 0.3379 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13466 Z= 0.151 Angle : 0.624 11.637 18238 Z= 0.315 Chirality : 0.043 0.146 1950 Planarity : 0.005 0.107 2360 Dihedral : 4.444 18.651 1812 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.43 % Allowed : 16.36 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1606 helix: 1.10 (0.19), residues: 786 sheet: -1.16 (0.38), residues: 166 loop : -0.64 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 704 TYR 0.021 0.002 TYR B 319 PHE 0.019 0.001 PHE A 270 TRP 0.016 0.001 TRP D 287 HIS 0.004 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00347 (13458) covalent geometry : angle 0.62355 (18234) SS BOND : bond 0.00970 ( 2) SS BOND : angle 1.89790 ( 4) hydrogen bonds : bond 0.03908 ( 600) hydrogen bonds : angle 4.50585 ( 1767) metal coordination : bond 0.00313 ( 6) *********************** 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 256 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7887 (tp30) cc_final: 0.7144 (tp30) REVERT: A 82 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: A 215 ARG cc_start: 0.7672 (ptp90) cc_final: 0.7193 (ttm110) REVERT: A 324 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6966 (tm-30) REVERT: A 606 ASP cc_start: 0.8403 (t70) cc_final: 0.8060 (t70) REVERT: B 229 VAL cc_start: 0.8814 (t) cc_final: 0.8422 (m) REVERT: B 231 MET cc_start: 0.6923 (pmm) cc_final: 0.6475 (pmm) REVERT: B 363 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: C 64 GLU cc_start: 0.7789 (tp30) cc_final: 0.6916 (tp30) REVERT: C 76 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7668 (mtm-85) REVERT: C 215 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7525 (ttm110) REVERT: C 311 ASP cc_start: 0.8159 (p0) cc_final: 0.7737 (p0) REVERT: D 229 VAL cc_start: 0.8631 (t) cc_final: 0.8094 (m) REVERT: D 314 ASP cc_start: 0.9054 (p0) cc_final: 0.8766 (p0) REVERT: D 339 ASP cc_start: 0.8161 (p0) cc_final: 0.7329 (p0) REVERT: D 340 GLU cc_start: 0.8126 (mp0) cc_final: 0.7544 (mp0) outliers start: 20 outliers final: 13 residues processed: 246 average time/residue: 0.6281 time to fit residues: 168.3606 Evaluate side-chains 247 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 265 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 B residue 367 GLN Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 292 GLU 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 62 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 148 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** 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 = 0.3755 r_free = 0.3755 target = 0.112127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096262 restraints weight = 22606.228| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.17 r_work: 0.3379 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2064 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= 0.144 Angle : 0.627 10.413 18238 Z= 0.318 Chirality : 0.043 0.143 1950 Planarity : 0.005 0.084 2360 Dihedral : 4.447 18.749 1812 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.22 % Allowed : 16.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1606 helix: 1.12 (0.19), residues: 786 sheet: -1.16 (0.39), residues: 166 loop : -0.65 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 704 TYR 0.023 0.001 TYR B 319 PHE 0.038 0.001 PHE A 270 TRP 0.017 0.001 TRP D 287 HIS 0.005 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00332 (13458) covalent geometry : angle 0.62690 (18234) SS BOND : bond 0.00901 ( 2) SS BOND : angle 1.79037 ( 4) hydrogen bonds : bond 0.03866 ( 600) hydrogen bonds : angle 4.49914 ( 1767) metal coordination : bond 0.00278 ( 6) ********************** 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 245 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7891 (tp30) cc_final: 0.7152 (tp30) REVERT: A 82 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: A 215 ARG cc_start: 0.7683 (ptp90) cc_final: 0.7202 (ttm110) REVERT: A 324 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6977 (tm-30) REVERT: B 229 VAL cc_start: 0.8845 (t) cc_final: 0.8443 (m) REVERT: B 231 MET cc_start: 0.6951 (pmm) cc_final: 0.6428 (pmm) REVERT: B 363 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: C 64 GLU cc_start: 0.7794 (tp30) cc_final: 0.6923 (tp30) REVERT: C 76 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7667 (mtm-85) REVERT: C 82 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: C 92 SER cc_start: 0.9060 (t) cc_final: 0.8838 (t) REVERT: C 215 ARG cc_start: 0.7839 (ptp-170) cc_final: 0.7542 (ttm110) REVERT: C 311 ASP cc_start: 0.8133 (p0) cc_final: 0.7753 (p0) REVERT: D 229 VAL cc_start: 0.8648 (t) cc_final: 0.8100 (m) REVERT: D 314 ASP cc_start: 0.9043 (p0) cc_final: 0.8778 (p0) REVERT: D 336 MET cc_start: 0.9132 (mtp) cc_final: 0.8929 (mtp) outliers start: 17 outliers final: 11 residues processed: 239 average time/residue: 0.5749 time to fit residues: 149.9698 Evaluate side-chains 243 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 76 ARG Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 212 ARG Chi-restraints excluded: chain D residue 292 GLU 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 122 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 120 optimal weight: 0.0770 chunk 99 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 HIS ** 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 = 0.3757 r_free = 0.3757 target = 0.111769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096001 restraints weight = 22487.859| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.16 r_work: 0.3387 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13466 Z= 0.142 Angle : 0.625 10.239 18238 Z= 0.319 Chirality : 0.042 0.146 1950 Planarity : 0.005 0.082 2360 Dihedral : 4.452 18.735 1812 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.15 % Allowed : 17.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1606 helix: 1.10 (0.19), residues: 786 sheet: -1.18 (0.39), residues: 166 loop : -0.66 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 704 TYR 0.021 0.001 TYR C 612 PHE 0.037 0.001 PHE A 270 TRP 0.019 0.001 TRP D 287 HIS 0.006 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00328 (13458) covalent geometry : angle 0.62443 (18234) SS BOND : bond 0.00966 ( 2) SS BOND : angle 1.60322 ( 4) hydrogen bonds : bond 0.03840 ( 600) hydrogen bonds : angle 4.49823 ( 1767) metal coordination : bond 0.00261 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5998.49 seconds wall clock time: 102 minutes 54.26 seconds (6174.26 seconds total)