Starting phenix.real_space_refine on Fri Oct 10 23:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teh_41186/10_2025/8teh_41186.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teh_41186/10_2025/8teh_41186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8teh_41186/10_2025/8teh_41186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teh_41186/10_2025/8teh_41186.map" model { file = "/net/cci-nas-00/data/ceres_data/8teh_41186/10_2025/8teh_41186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teh_41186/10_2025/8teh_41186.cif" } resolution = 2.3 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= 0.000 sd= 0.007 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 P 16 5.49 5 S 60 5.16 5 C 6458 2.51 5 N 1432 2.21 5 O 1850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9816 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4374 Classifications: {'peptide': 554} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 518} Chain breaks: 2 Chain: "B" Number of atoms: 4374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4374 Classifications: {'peptide': 554} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 518} Chain breaks: 2 Chain: "A" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 442 Unusual residues: {'POV': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 412 Unusual residues: {'POV': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Time building chain proxies: 2.28, per 1000 atoms: 0.23 Number of scatterers: 9816 At special positions: 0 Unit cell: (85.49, 125.33, 85.49, 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) S 60 16.00 P 16 15.00 O 1850 8.00 N 1432 7.00 C 6458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 295.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 78.5% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.867A pdb=" N MET A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.770A pdb=" N GLY A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 62 removed outlier: 3.697A pdb=" N ILE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.546A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 151 removed outlier: 4.995A pdb=" N ASN A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.634A pdb=" N SER A 223 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 252 removed outlier: 6.349A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.640A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.542A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 297 through 320 removed outlier: 3.563A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.593A pdb=" N LEU A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.659A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 517 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.821A pdb=" N VAL A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 539 through 561 Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 576 Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.585A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.775A pdb=" N GLU A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 635 removed outlier: 3.882A pdb=" N GLU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.868A pdb=" N MET B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.771A pdb=" N GLY B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 62 removed outlier: 3.699A pdb=" N ILE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 67 through 86 Processing helix chain 'B' and resid 96 through 112 removed outlier: 3.545A pdb=" N ALA B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 120 through 142 Processing helix chain 'B' and resid 143 through 151 removed outlier: 4.995A pdb=" N ASN B 149 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 178 Processing helix chain 'B' and resid 189 through 192 Processing helix chain 'B' and resid 193 through 219 Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.634A pdb=" N SER B 223 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 6.349A pdb=" N VAL B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 253 through 258 removed outlier: 4.640A pdb=" N GLY B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.543A pdb=" N LEU B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 297 through 320 removed outlier: 3.564A pdb=" N MET B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 313 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 359 through 368 Processing helix chain 'B' and resid 464 through 480 removed outlier: 3.593A pdb=" N LEU B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.659A pdb=" N LEU B 492 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 517 Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 528 removed outlier: 3.821A pdb=" N VAL B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 539 through 561 Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 576 through 584 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.584A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 609 through 615 removed outlier: 3.776A pdb=" N GLU B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 635 removed outlier: 3.882A pdb=" N GLU B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 371 Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA4, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.173A pdb=" N HIS A 644 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'B' and resid 369 through 371 562 hydrogen bonds defined for protein. 1608 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: 1.39 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.63: 9701 1.63 - 2.05: 119 2.05 - 2.48: 0 2.48 - 2.90: 0 2.90 - 3.32: 2 Bond restraints: 9822 Sorted by residual: bond pdb="C214 POV A 804 " pdb="C215 POV A 804 " ideal model delta sigma weight residual 1.524 3.325 -1.801 2.00e-02 2.50e+03 8.11e+03 bond pdb="C214 POV B 810 " pdb="C215 POV B 810 " ideal model delta sigma weight residual 1.524 3.324 -1.800 2.00e-02 2.50e+03 8.10e+03 bond pdb=" C29 POV B 807 " pdb="C210 POV B 807 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C29 POV A 801 " pdb="C210 POV A 801 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C29 POV A 806 " pdb="C210 POV A 806 " ideal model delta sigma weight residual 1.333 1.526 -0.193 2.00e-02 2.50e+03 9.32e+01 ... (remaining 9817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 13072 2.78 - 5.56: 80 5.56 - 8.34: 0 8.34 - 11.12: 6 11.12 - 13.91: 10 Bond angle restraints: 13168 Sorted by residual: angle pdb=" C28 POV A 806 " pdb=" C29 POV A 806 " pdb="C210 POV A 806 " ideal model delta sigma weight residual 127.79 113.88 13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C28 POV A 811 " pdb=" C29 POV A 811 " pdb="C210 POV A 811 " ideal model delta sigma weight residual 127.79 113.92 13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C28 POV B 807 " pdb=" C29 POV B 807 " pdb="C210 POV B 807 " ideal model delta sigma weight residual 127.79 114.30 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C28 POV A 801 " pdb=" C29 POV A 801 " pdb="C210 POV A 801 " ideal model delta sigma weight residual 127.79 114.35 13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C29 POV A 801 " pdb="C210 POV A 801 " pdb="C211 POV A 801 " ideal model delta sigma weight residual 127.67 114.52 13.15 3.00e+00 1.11e-01 1.92e+01 ... (remaining 13163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 5511 34.74 - 69.49: 396 69.49 - 104.23: 47 104.23 - 138.97: 6 138.97 - 173.71: 4 Dihedral angle restraints: 5964 sinusoidal: 2778 harmonic: 3186 Sorted by residual: dihedral pdb=" C29 POV A 806 " pdb="C210 POV A 806 " pdb="C211 POV A 806 " pdb="C212 POV A 806 " ideal model delta sinusoidal sigma weight residual 112.25 -74.04 -173.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV A 811 " pdb="C210 POV A 811 " pdb="C211 POV A 811 " pdb="C212 POV A 811 " ideal model delta sinusoidal sigma weight residual 112.25 -74.05 -173.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C27 POV A 811 " pdb=" C28 POV A 811 " pdb=" C29 POV A 811 " pdb="C210 POV A 811 " ideal model delta sinusoidal sigma weight residual 127.48 -63.58 -168.94 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 5961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 896 0.028 - 0.056: 321 0.056 - 0.084: 111 0.084 - 0.112: 55 0.112 - 0.140: 15 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA PRO B 505 " pdb=" N PRO B 505 " pdb=" C PRO B 505 " pdb=" CB PRO B 505 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA PRO A 505 " pdb=" N PRO A 505 " pdb=" C PRO A 505 " pdb=" CB PRO A 505 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1395 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A 801 " 0.147 2.00e-02 2.50e+03 3.28e-01 1.07e+03 pdb=" C29 POV A 801 " -0.433 2.00e-02 2.50e+03 pdb="C210 POV A 801 " 0.443 2.00e-02 2.50e+03 pdb="C211 POV A 801 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 807 " -0.145 2.00e-02 2.50e+03 3.28e-01 1.07e+03 pdb=" C29 POV B 807 " 0.431 2.00e-02 2.50e+03 pdb="C210 POV B 807 " -0.445 2.00e-02 2.50e+03 pdb="C211 POV B 807 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 806 " 0.124 2.00e-02 2.50e+03 2.07e-01 4.30e+02 pdb=" C29 POV A 806 " -0.265 2.00e-02 2.50e+03 pdb="C210 POV A 806 " 0.266 2.00e-02 2.50e+03 pdb="C211 POV A 806 " -0.125 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 116 2.60 - 3.17: 8259 3.17 - 3.75: 15650 3.75 - 4.32: 23366 4.32 - 4.90: 37094 Nonbonded interactions: 84485 Sorted by model distance: nonbonded pdb=" O PHE A 558 " pdb=" OG1 THR A 561 " model vdw 2.021 3.040 nonbonded pdb=" O PHE B 558 " pdb=" OG1 THR B 561 " model vdw 2.021 3.040 nonbonded pdb=" OH TYR A 495 " pdb=" O HOH A 901 " model vdw 2.096 3.040 nonbonded pdb=" OH TYR B 495 " pdb=" O HOH B 901 " model vdw 2.098 3.040 nonbonded pdb=" O GLN B 463 " pdb=" O HOH B 902 " model vdw 2.152 3.040 ... (remaining 84480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 645 or (resid 801 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O21 or name O22 or name C210 or name C211 or name C212)) or (resid 802 a \ nd (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C \ 25 or name C26 or name C27 or name C28 or name C29)) or (resid 803 and (name C1 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C3 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name C310)) \ or (resid 804 and (name N or name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or n \ ame O32 or name P or name C210 or name C211)) or (resid 805 and (name N or name \ C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or nam \ e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name O31 or name O32 or name P or name C310 or name C311)) o \ r resid 806 or (resid 807 and (name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C26 or name C27 or name C28 or name C29 or name O21 or name O22 \ or name C210 or name C211 or name C212)) or (resid 808 and (name C1 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29)) or (resid 809 and (name C1 or name C2 or name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39 or name O11 or name C310)) or resid 810 or (resid \ 811 and (name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ name C28 or name C29 or name C210 or name C211 or name C212 or name C213)))) selection = (chain 'B' and (resid 5 through 645 or (resid 801 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O21 or name O22 or name C210 or name C211 or name C212)) or (resid 802 a \ nd (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C \ 25 or name C26 or name C27 or name C28 or name C29)) or (resid 803 and (name C1 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C3 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name C310)) \ or resid 804 through 805 or (resid 806 and (name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C210 or name C \ 211 or name C212 or name C213 or name C214 or name C215 or name C216)) or (resid \ 807 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 o \ r name C27 or name C28 or name C29 or name O21 or name O22 or name C210 or name \ C211 or name C212)) or (resid 808 and (name C1 or name C2 or name C21 or name C2 \ 2 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or nam \ e C29)) or (resid 809 and (name C1 or name C2 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name O11 or name C310)) or (resid 810 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or na \ me O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211)) \ or (resid 811 and (name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C210 or name C211 or name C212 or name \ C213)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.026 1.801 9824 Z= 1.310 Angle : 0.667 13.905 13168 Z= 0.286 Chirality : 0.037 0.140 1398 Planarity : 0.014 0.328 1578 Dihedral : 22.406 173.714 3916 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.43 % Allowed : 11.54 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.42 (0.25), residues: 1096 helix: 1.11 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.86 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.007 0.001 TYR A 22 PHE 0.010 0.001 PHE B 298 TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS B 644 Details of bonding type rmsd covalent geometry : bond 0.02622 ( 9822) covalent geometry : angle 0.66707 (13168) hydrogen bonds : bond 0.13611 ( 562) hydrogen bonds : angle 5.48904 ( 1608) Misc. bond : bond 0.01819 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.287 Fit side-chains REVERT: A 187 GLN cc_start: 0.7238 (mt0) cc_final: 0.6997 (mm-40) REVERT: A 220 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7244 (tptp) REVERT: A 267 PHE cc_start: 0.7786 (m-80) cc_final: 0.7550 (m-10) REVERT: A 573 MET cc_start: 0.7954 (mmm) cc_final: 0.7578 (mmm) REVERT: B 187 GLN cc_start: 0.7325 (mt0) cc_final: 0.7072 (mm-40) REVERT: B 220 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7295 (tptp) REVERT: B 267 PHE cc_start: 0.7749 (m-80) cc_final: 0.7531 (m-10) REVERT: B 573 MET cc_start: 0.7932 (mmm) cc_final: 0.7549 (mmm) REVERT: B 587 ARG cc_start: 0.7241 (mtt-85) cc_final: 0.6980 (mtp180) outliers start: 4 outliers final: 4 residues processed: 123 average time/residue: 0.6534 time to fit residues: 85.3456 Evaluate side-chains 121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN A 644 HIS B 24 GLN B 595 GLN B 644 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.140124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.107629 restraints weight = 7938.347| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.05 r_work: 0.2915 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9824 Z= 0.222 Angle : 0.735 8.186 13168 Z= 0.368 Chirality : 0.049 0.193 1398 Planarity : 0.005 0.038 1578 Dihedral : 23.592 127.002 1880 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.71 % Allowed : 10.36 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.34 (0.25), residues: 1096 helix: 1.05 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.82 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 184 TYR 0.015 0.003 TYR B 495 PHE 0.024 0.002 PHE A 209 TRP 0.012 0.002 TRP A 131 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9822) covalent geometry : angle 0.73543 (13168) hydrogen bonds : bond 0.07519 ( 562) hydrogen bonds : angle 5.07730 ( 1608) Misc. bond : bond 0.00265 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.212 Fit side-chains REVERT: A 187 GLN cc_start: 0.7302 (mt0) cc_final: 0.6880 (mm-40) REVERT: A 220 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7970 (mppt) REVERT: A 285 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 463 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7603 (pp30) REVERT: A 541 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7574 (ttpt) REVERT: A 584 LEU cc_start: 0.8476 (mt) cc_final: 0.8239 (mm) REVERT: A 603 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: B 20 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7595 (mmm) REVERT: B 187 GLN cc_start: 0.7314 (mt0) cc_final: 0.6947 (mm-40) REVERT: B 220 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7971 (mppt) REVERT: B 285 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: B 463 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7609 (pp30) REVERT: B 541 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7570 (ttpt) REVERT: B 582 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: B 603 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8062 (mm-30) outliers start: 16 outliers final: 1 residues processed: 131 average time/residue: 0.6626 time to fit residues: 91.9787 Evaluate side-chains 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.109554 restraints weight = 8084.330| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.06 r_work: 0.2944 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9824 Z= 0.150 Angle : 0.580 8.069 13168 Z= 0.296 Chirality : 0.043 0.165 1398 Planarity : 0.004 0.036 1578 Dihedral : 22.377 117.406 1874 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.28 % Allowed : 11.32 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.53 (0.25), residues: 1096 helix: 1.28 (0.19), residues: 746 sheet: -3.18 (0.77), residues: 20 loop : 0.97 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 184 TYR 0.012 0.002 TYR B 495 PHE 0.013 0.002 PHE B 209 TRP 0.013 0.002 TRP A 247 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9822) covalent geometry : angle 0.57996 (13168) hydrogen bonds : bond 0.06176 ( 562) hydrogen bonds : angle 4.81072 ( 1608) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.358 Fit side-chains REVERT: A 20 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7584 (mmm) REVERT: A 187 GLN cc_start: 0.7296 (mt0) cc_final: 0.6886 (mm-40) REVERT: A 285 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: A 463 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7367 (pp30) REVERT: A 584 LEU cc_start: 0.8448 (mt) cc_final: 0.8236 (mm) REVERT: B 187 GLN cc_start: 0.7328 (mt0) cc_final: 0.6877 (mm-40) REVERT: B 285 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: B 463 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7354 (pp30) REVERT: B 582 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7903 (mp10) REVERT: B 603 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8004 (mm-30) outliers start: 12 outliers final: 0 residues processed: 127 average time/residue: 0.6586 time to fit residues: 88.6736 Evaluate side-chains 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 0.0030 chunk 58 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113461 restraints weight = 8225.522| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.06 r_work: 0.3009 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9824 Z= 0.113 Angle : 0.503 7.294 13168 Z= 0.254 Chirality : 0.040 0.144 1398 Planarity : 0.004 0.032 1578 Dihedral : 21.006 108.321 1874 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.39 % Allowed : 12.50 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.94 (0.25), residues: 1096 helix: 1.55 (0.19), residues: 760 sheet: -3.12 (0.82), residues: 20 loop : 1.22 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 327 TYR 0.007 0.001 TYR A 495 PHE 0.013 0.001 PHE B 534 TRP 0.014 0.001 TRP B 247 HIS 0.003 0.001 HIS B 644 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9822) covalent geometry : angle 0.50320 (13168) hydrogen bonds : bond 0.04824 ( 562) hydrogen bonds : angle 4.51063 ( 1608) Misc. bond : bond 0.00001 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.350 Fit side-chains REVERT: A 187 GLN cc_start: 0.7324 (mt0) cc_final: 0.6879 (mm-40) REVERT: A 285 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: A 463 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7153 (pp30) REVERT: B 20 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7540 (mmm) REVERT: B 119 ASP cc_start: 0.7914 (m-30) cc_final: 0.7616 (m-30) REVERT: B 187 GLN cc_start: 0.7311 (mt0) cc_final: 0.6866 (mm-40) REVERT: B 285 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: B 463 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7141 (pp30) REVERT: B 582 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7833 (mp10) outliers start: 13 outliers final: 2 residues processed: 136 average time/residue: 0.6594 time to fit residues: 95.1901 Evaluate side-chains 126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 582 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.109409 restraints weight = 8143.245| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.06 r_work: 0.2947 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9824 Z= 0.149 Angle : 0.579 7.819 13168 Z= 0.294 Chirality : 0.043 0.157 1398 Planarity : 0.004 0.036 1578 Dihedral : 21.019 105.489 1874 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.60 % Allowed : 11.86 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.70 (0.25), residues: 1096 helix: 1.34 (0.19), residues: 762 sheet: -3.01 (0.86), residues: 20 loop : 1.22 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.011 0.002 TYR B 495 PHE 0.014 0.002 PHE A 209 TRP 0.010 0.001 TRP B 247 HIS 0.004 0.001 HIS B 644 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9822) covalent geometry : angle 0.57934 (13168) hydrogen bonds : bond 0.06220 ( 562) hydrogen bonds : angle 4.74249 ( 1608) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.344 Fit side-chains REVERT: A 20 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7521 (mmm) REVERT: A 187 GLN cc_start: 0.7265 (mt0) cc_final: 0.6794 (mm-40) REVERT: A 285 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 463 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7400 (pp30) REVERT: A 541 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7552 (ttpt) REVERT: B 20 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7530 (mmm) REVERT: B 187 GLN cc_start: 0.7289 (mt0) cc_final: 0.6809 (mm-40) REVERT: B 285 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: B 463 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7491 (pp30) REVERT: B 541 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7560 (ttpt) REVERT: B 603 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8003 (mm-30) outliers start: 15 outliers final: 0 residues processed: 125 average time/residue: 0.6705 time to fit residues: 88.8752 Evaluate side-chains 126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110416 restraints weight = 8242.667| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.16 r_work: 0.2931 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9824 Z= 0.159 Angle : 0.601 8.085 13168 Z= 0.306 Chirality : 0.044 0.158 1398 Planarity : 0.005 0.038 1578 Dihedral : 21.107 111.634 1874 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.82 % Allowed : 11.97 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.58 (0.25), residues: 1096 helix: 1.32 (0.19), residues: 748 sheet: -2.99 (0.86), residues: 20 loop : 0.97 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 184 TYR 0.012 0.002 TYR A 495 PHE 0.014 0.002 PHE A 209 TRP 0.011 0.002 TRP B 247 HIS 0.003 0.001 HIS B 644 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9822) covalent geometry : angle 0.60134 (13168) hydrogen bonds : bond 0.06446 ( 562) hydrogen bonds : angle 4.81103 ( 1608) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.300 Fit side-chains REVERT: A 285 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: A 327 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7271 (mtm-85) REVERT: A 463 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7544 (pp30) REVERT: A 541 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7606 (ttpt) REVERT: A 603 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: B 20 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7547 (mmm) REVERT: B 285 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: B 327 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7254 (mtm-85) REVERT: B 463 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7426 (pp30) REVERT: B 541 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7614 (ttpt) REVERT: B 603 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7990 (mm-30) outliers start: 17 outliers final: 0 residues processed: 125 average time/residue: 0.7062 time to fit residues: 93.3137 Evaluate side-chains 125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 541 LYS Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111027 restraints weight = 8188.931| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.15 r_work: 0.2971 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9824 Z= 0.127 Angle : 0.535 7.741 13168 Z= 0.271 Chirality : 0.042 0.151 1398 Planarity : 0.004 0.035 1578 Dihedral : 20.193 111.467 1874 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.07 % Allowed : 12.71 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.79 (0.25), residues: 1096 helix: 1.43 (0.19), residues: 762 sheet: -2.92 (0.88), residues: 20 loop : 1.19 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 184 TYR 0.009 0.001 TYR A 495 PHE 0.013 0.001 PHE A 534 TRP 0.014 0.001 TRP B 247 HIS 0.003 0.001 HIS B 644 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9822) covalent geometry : angle 0.53514 (13168) hydrogen bonds : bond 0.05435 ( 562) hydrogen bonds : angle 4.57749 ( 1608) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.369 Fit side-chains REVERT: A 20 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7558 (mmm) REVERT: A 285 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: A 463 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7294 (pp30) REVERT: B 20 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7551 (mmm) REVERT: B 285 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: B 463 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7296 (pp30) REVERT: B 603 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8008 (mm-30) outliers start: 10 outliers final: 2 residues processed: 121 average time/residue: 0.6147 time to fit residues: 79.2395 Evaluate side-chains 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 105 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115428 restraints weight = 8244.885| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.06 r_work: 0.3020 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9824 Z= 0.116 Angle : 0.510 7.492 13168 Z= 0.257 Chirality : 0.041 0.146 1398 Planarity : 0.004 0.036 1578 Dihedral : 19.360 109.104 1874 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.18 % Allowed : 12.82 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 2.00 (0.25), residues: 1096 helix: 1.59 (0.19), residues: 762 sheet: -3.04 (0.85), residues: 20 loop : 1.26 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 327 TYR 0.007 0.001 TYR A 495 PHE 0.012 0.001 PHE B 534 TRP 0.015 0.001 TRP B 247 HIS 0.002 0.001 HIS B 644 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9822) covalent geometry : angle 0.51029 (13168) hydrogen bonds : bond 0.04931 ( 562) hydrogen bonds : angle 4.43155 ( 1608) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.329 Fit side-chains REVERT: A 187 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6932 (mm-40) REVERT: A 285 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 463 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7298 (pp30) REVERT: B 20 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7469 (mmm) REVERT: B 187 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6938 (mm-40) REVERT: B 285 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: B 463 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7213 (pp30) REVERT: B 603 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7923 (mm-30) outliers start: 11 outliers final: 2 residues processed: 125 average time/residue: 0.6633 time to fit residues: 88.1055 Evaluate side-chains 126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110208 restraints weight = 8156.135| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.13 r_work: 0.2936 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9824 Z= 0.166 Angle : 0.608 8.000 13168 Z= 0.308 Chirality : 0.044 0.161 1398 Planarity : 0.005 0.038 1578 Dihedral : 19.898 112.929 1874 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.50 % Allowed : 12.61 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.65 (0.25), residues: 1096 helix: 1.36 (0.19), residues: 752 sheet: -2.99 (0.87), residues: 20 loop : 1.04 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 184 TYR 0.011 0.002 TYR A 495 PHE 0.015 0.002 PHE B 209 TRP 0.010 0.002 TRP B 247 HIS 0.004 0.001 HIS B 644 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9822) covalent geometry : angle 0.60755 (13168) hydrogen bonds : bond 0.06503 ( 562) hydrogen bonds : angle 4.73692 ( 1608) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.247 Fit side-chains REVERT: A 20 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7511 (mmm) REVERT: A 285 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 327 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7238 (mtm-85) REVERT: A 463 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7479 (pp30) REVERT: A 603 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: B 20 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7535 (mmm) REVERT: B 285 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: B 327 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7285 (mtm-85) REVERT: B 463 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7485 (pp30) REVERT: B 603 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7967 (mm-30) outliers start: 14 outliers final: 0 residues processed: 124 average time/residue: 0.6805 time to fit residues: 89.3391 Evaluate side-chains 125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 94 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.114961 restraints weight = 8194.007| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.08 r_work: 0.3015 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9824 Z= 0.115 Angle : 0.513 7.640 13168 Z= 0.259 Chirality : 0.041 0.141 1398 Planarity : 0.004 0.035 1578 Dihedral : 19.023 111.068 1874 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.96 % Allowed : 13.03 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 1.96 (0.25), residues: 1096 helix: 1.57 (0.19), residues: 762 sheet: -3.00 (0.88), residues: 20 loop : 1.22 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 327 TYR 0.007 0.001 TYR A 495 PHE 0.013 0.001 PHE B 534 TRP 0.015 0.001 TRP A 247 HIS 0.003 0.001 HIS B 644 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9822) covalent geometry : angle 0.51343 (13168) hydrogen bonds : bond 0.04955 ( 562) hydrogen bonds : angle 4.45803 ( 1608) Misc. bond : bond 0.00007 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.275 Fit side-chains REVERT: A 20 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7472 (mmm) REVERT: A 285 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 463 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7312 (pp30) REVERT: A 603 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: B 20 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: B 285 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: B 463 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7323 (pp30) REVERT: B 603 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7945 (mm-30) outliers start: 9 outliers final: 0 residues processed: 122 average time/residue: 0.5936 time to fit residues: 77.0784 Evaluate side-chains 124 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118016 restraints weight = 8277.352| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.07 r_work: 0.3071 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9824 Z= 0.105 Angle : 0.487 7.069 13168 Z= 0.244 Chirality : 0.040 0.134 1398 Planarity : 0.004 0.035 1578 Dihedral : 17.969 108.065 1874 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.64 % Allowed : 13.57 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 2.26 (0.26), residues: 1096 helix: 1.81 (0.19), residues: 762 sheet: -3.11 (0.90), residues: 20 loop : 1.31 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 643 TYR 0.008 0.001 TYR B 22 PHE 0.012 0.001 PHE B 534 TRP 0.016 0.001 TRP B 247 HIS 0.002 0.001 HIS A 644 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9822) covalent geometry : angle 0.48712 (13168) hydrogen bonds : bond 0.04305 ( 562) hydrogen bonds : angle 4.28258 ( 1608) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3815.34 seconds wall clock time: 65 minutes 36.70 seconds (3936.70 seconds total)