Starting phenix.real_space_refine on Fri Feb 14 04:34:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teh_41186/02_2025/8teh_41186.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teh_41186/02_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_41186/02_2025/8teh_41186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teh_41186/02_2025/8teh_41186.map" model { file = "/net/cci-nas-00/data/ceres_data/8teh_41186/02_2025/8teh_41186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teh_41186/02_2025/8teh_41186.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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-3': 2, 'POV:plan-1': 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: 5.81, per 1000 atoms: 0.59 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.21 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: 2.70 Time building geometry restraints manager: 3.02 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: 1.350 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.520 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- 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 9822 Z= 1.140 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (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 TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS B 644 PHE 0.010 0.001 PHE B 298 TYR 0.007 0.001 TYR A 22 ARG 0.002 0.000 ARG A 180 *********************** 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 : 1.023 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: 1.5406 time to fit residues: 201.3024 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 : 1.082 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 595 GLN B 644 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.111083 restraints weight = 7906.037| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.05 r_work: 0.2969 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9822 Z= 0.201 Angle : 0.614 7.566 13168 Z= 0.306 Chirality : 0.044 0.174 1398 Planarity : 0.005 0.034 1578 Dihedral : 23.068 126.406 1880 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.39 % Allowed : 10.36 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1096 helix: 1.34 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.95 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 247 HIS 0.004 0.001 HIS B 312 PHE 0.015 0.002 PHE B 209 TYR 0.009 0.002 TYR A 495 ARG 0.003 0.001 ARG A 327 *********************** 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 140 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.089 Fit side-chains REVERT: A 187 GLN cc_start: 0.7173 (mt0) cc_final: 0.6834 (mm-40) REVERT: A 220 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7888 (mppt) REVERT: A 285 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 463 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7394 (pp30) REVERT: A 517 PHE cc_start: 0.7903 (m-80) cc_final: 0.7634 (m-80) REVERT: A 582 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: A 603 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8055 (mm-30) REVERT: B 187 GLN cc_start: 0.7184 (mt0) cc_final: 0.6843 (mm-40) REVERT: B 220 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7883 (mppt) REVERT: B 285 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: B 463 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7384 (pp30) REVERT: B 517 PHE cc_start: 0.7883 (m-80) cc_final: 0.7622 (m-80) REVERT: B 582 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: B 584 LEU cc_start: 0.8314 (mt) cc_final: 0.8105 (mm) REVERT: B 603 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7955 (mm-30) outliers start: 13 outliers final: 0 residues processed: 133 average time/residue: 1.5799 time to fit residues: 222.8815 Evaluate side-chains 127 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 603 GLU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.141987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.109525 restraints weight = 8097.246| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.14 r_work: 0.2945 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9822 Z= 0.198 Angle : 0.588 7.549 13168 Z= 0.298 Chirality : 0.043 0.162 1398 Planarity : 0.004 0.037 1578 Dihedral : 22.220 115.538 1874 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.92 % Allowed : 10.79 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.25), residues: 1096 helix: 1.34 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.96 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 247 HIS 0.003 0.001 HIS A 364 PHE 0.016 0.002 PHE A 209 TYR 0.011 0.002 TYR A 495 ARG 0.003 0.001 ARG A 184 *********************** 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 142 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.017 Fit side-chains REVERT: A 20 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7520 (mmm) REVERT: A 187 GLN cc_start: 0.7199 (mt0) cc_final: 0.6837 (mm-40) REVERT: A 285 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: A 463 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7486 (pp30) REVERT: A 541 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7520 (ttpt) REVERT: A 582 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: A 603 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: B 20 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: B 119 ASP cc_start: 0.7816 (m-30) cc_final: 0.7570 (m-30) REVERT: B 187 GLN cc_start: 0.7211 (mt0) cc_final: 0.6841 (mm-40) REVERT: B 285 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 463 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7479 (pp30) REVERT: B 541 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7532 (ttpt) REVERT: B 582 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: B 584 LEU cc_start: 0.8453 (mt) cc_final: 0.8244 (mm) REVERT: B 603 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7942 (mm-30) outliers start: 18 outliers final: 2 residues processed: 133 average time/residue: 1.5867 time to fit residues: 223.8268 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 : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 582 GLN Chi-restraints excluded: chain A residue 603 GLU 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 541 LYS 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 74 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.140825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108433 restraints weight = 8031.946| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.13 r_work: 0.2921 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9822 Z= 0.231 Angle : 0.620 7.877 13168 Z= 0.315 Chirality : 0.045 0.157 1398 Planarity : 0.005 0.038 1578 Dihedral : 21.796 109.340 1874 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.92 % Allowed : 11.65 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1096 helix: 1.23 (0.19), residues: 748 sheet: -2.72 (0.90), residues: 20 loop : 0.97 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 247 HIS 0.004 0.001 HIS B 644 PHE 0.018 0.002 PHE A 209 TYR 0.013 0.002 TYR B 495 ARG 0.004 0.001 ARG A 184 *********************** 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 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.166 Fit side-chains REVERT: A 20 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7589 (mmm) REVERT: A 285 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: A 463 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7426 (pp30) REVERT: A 541 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7601 (ttpt) REVERT: A 582 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: A 603 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: B 20 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7581 (mmm) REVERT: B 285 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: B 463 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7427 (pp30) REVERT: B 541 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7635 (ttpt) REVERT: B 582 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: B 584 LEU cc_start: 0.8496 (mt) cc_final: 0.8269 (mm) REVERT: B 603 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8023 (mm-30) outliers start: 18 outliers final: 0 residues processed: 128 average time/residue: 1.4918 time to fit residues: 203.0990 Evaluate side-chains 126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 582 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 541 LYS Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.141885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109579 restraints weight = 8093.552| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.05 r_work: 0.2944 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9822 Z= 0.194 Angle : 0.574 7.819 13168 Z= 0.292 Chirality : 0.043 0.159 1398 Planarity : 0.004 0.038 1578 Dihedral : 21.007 110.525 1874 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.46 % Allowed : 11.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1096 helix: 1.36 (0.19), residues: 748 sheet: -2.79 (0.82), residues: 20 loop : 0.97 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 247 HIS 0.003 0.001 HIS B 644 PHE 0.013 0.001 PHE A 298 TYR 0.012 0.002 TYR A 495 ARG 0.003 0.000 ARG A 184 *********************** 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 138 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.994 Fit side-chains REVERT: A 20 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7571 (mmm) REVERT: A 285 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: A 327 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7243 (mtm-85) REVERT: A 463 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7492 (pp30) REVERT: A 541 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7595 (ttpt) REVERT: A 582 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: A 603 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: B 20 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7570 (mmm) REVERT: B 285 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: B 327 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7255 (mtm-85) REVERT: B 463 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7492 (pp30) REVERT: B 541 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7608 (ttpt) REVERT: B 582 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: B 584 LEU cc_start: 0.8493 (mt) cc_final: 0.8289 (mm) REVERT: B 603 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7959 (mm-30) outliers start: 23 outliers final: 4 residues processed: 128 average time/residue: 1.6921 time to fit residues: 229.5738 Evaluate side-chains 138 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 327 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 603 GLU 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 327 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.140703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109674 restraints weight = 8126.653| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.12 r_work: 0.2929 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9822 Z= 0.227 Angle : 0.622 8.011 13168 Z= 0.315 Chirality : 0.045 0.161 1398 Planarity : 0.005 0.039 1578 Dihedral : 20.997 113.681 1874 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.92 % Allowed : 11.22 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1096 helix: 1.23 (0.19), residues: 748 sheet: -2.93 (0.84), residues: 20 loop : 0.90 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 247 HIS 0.004 0.001 HIS A 644 PHE 0.016 0.002 PHE A 209 TYR 0.013 0.002 TYR B 495 ARG 0.003 0.000 ARG A 184 *********************** 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 139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.066 Fit side-chains REVERT: A 20 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7587 (mmm) REVERT: A 285 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: A 327 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7252 (mtm-85) REVERT: A 463 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7419 (pp30) REVERT: A 541 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7616 (ttpt) REVERT: A 582 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: A 603 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8113 (mm-30) REVERT: B 20 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7574 (mmm) REVERT: B 285 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: B 327 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7267 (mtm-85) REVERT: B 463 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7424 (pp30) REVERT: B 541 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7601 (ttpt) REVERT: B 582 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: B 603 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7995 (mm-30) outliers start: 18 outliers final: 2 residues processed: 131 average time/residue: 1.5548 time to fit residues: 216.1528 Evaluate side-chains 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 541 LYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 603 GLU 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 327 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 25 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.143302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.112412 restraints weight = 8229.009| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.13 r_work: 0.2978 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 0.029 9822 Z= 0.158 Angle : 0.536 7.762 13168 Z= 0.272 Chirality : 0.042 0.147 1398 Planarity : 0.004 0.036 1578 Dihedral : 20.095 112.204 1874 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.92 % Allowed : 11.43 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1096 helix: 1.49 (0.19), residues: 750 sheet: -2.98 (0.84), residues: 20 loop : 1.00 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 247 HIS 0.005 0.001 HIS A 644 PHE 0.013 0.001 PHE B 534 TYR 0.008 0.001 TYR A 495 ARG 0.002 0.000 ARG B 184 *********************** 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 139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.061 Fit side-chains REVERT: A 20 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7552 (mmm) REVERT: A 285 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: A 327 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7286 (mtm-85) REVERT: A 463 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7405 (pp30) REVERT: A 582 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: B 20 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7552 (mmm) REVERT: B 285 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: B 327 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7242 (mtm-85) REVERT: B 463 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7413 (pp30) REVERT: B 582 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7823 (mp10) outliers start: 18 outliers final: 2 residues processed: 131 average time/residue: 1.5208 time to fit residues: 211.8917 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 : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 582 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 327 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 582 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 72 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.144990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115739 restraints weight = 8245.445| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.04 r_work: 0.3025 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9822 Z= 0.141 Angle : 0.509 7.329 13168 Z= 0.257 Chirality : 0.041 0.141 1398 Planarity : 0.004 0.036 1578 Dihedral : 19.122 109.457 1874 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.39 % Allowed : 12.29 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.25), residues: 1096 helix: 1.57 (0.19), residues: 762 sheet: -2.96 (0.86), residues: 20 loop : 1.19 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 247 HIS 0.003 0.001 HIS A 644 PHE 0.013 0.001 PHE A 298 TYR 0.007 0.001 TYR A 495 ARG 0.002 0.000 ARG A 327 *********************** 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 136 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.069 Fit side-chains REVERT: A 20 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7508 (mmm) REVERT: A 285 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: A 463 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7202 (pp30) REVERT: A 582 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: B 20 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7508 (mmm) REVERT: B 285 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: B 463 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7204 (pp30) REVERT: B 582 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7924 (mp10) outliers start: 13 outliers final: 2 residues processed: 127 average time/residue: 1.4319 time to fit residues: 193.9212 Evaluate side-chains 132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 582 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.143184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112893 restraints weight = 8198.230| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.09 r_work: 0.2980 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9822 Z= 0.163 Angle : 0.539 7.739 13168 Z= 0.274 Chirality : 0.042 0.148 1398 Planarity : 0.004 0.037 1578 Dihedral : 18.986 109.688 1874 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.60 % Allowed : 12.71 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.25), residues: 1096 helix: 1.56 (0.19), residues: 750 sheet: -2.95 (0.86), residues: 20 loop : 1.06 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.004 0.001 HIS A 644 PHE 0.012 0.001 PHE B 534 TYR 0.009 0.001 TYR A 495 ARG 0.002 0.000 ARG A 184 *********************** 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 135 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.042 Fit side-chains REVERT: A 20 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7502 (mmm) REVERT: A 285 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: A 327 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7216 (mtm-85) REVERT: A 463 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7372 (pp30) REVERT: A 541 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7541 (ttpt) REVERT: B 20 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7497 (mmm) REVERT: B 285 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: B 327 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7219 (mtm-85) REVERT: B 463 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7369 (pp30) REVERT: B 541 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7561 (ttpt) REVERT: B 582 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: B 603 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7950 (mm-30) outliers start: 15 outliers final: 2 residues processed: 127 average time/residue: 1.5925 time to fit residues: 214.6991 Evaluate side-chains 132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 541 LYS 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 327 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 105 optimal weight: 0.0040 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.147035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117054 restraints weight = 8301.434| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.13 r_work: 0.3043 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9822 Z= 0.129 Angle : 0.489 7.219 13168 Z= 0.246 Chirality : 0.040 0.137 1398 Planarity : 0.004 0.035 1578 Dihedral : 18.162 107.931 1874 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.07 % Allowed : 13.25 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.25), residues: 1096 helix: 1.77 (0.19), residues: 760 sheet: -3.06 (0.89), residues: 20 loop : 1.23 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 247 HIS 0.002 0.001 HIS B 333 PHE 0.013 0.001 PHE B 534 TYR 0.007 0.001 TYR A 22 ARG 0.002 0.000 ARG A 327 ********************** 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 136 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.089 Fit side-chains REVERT: A 20 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7480 (mmm) REVERT: A 24 GLN cc_start: 0.7687 (mp-120) cc_final: 0.6983 (tm-30) REVERT: A 285 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: A 463 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7078 (pp30) REVERT: B 24 GLN cc_start: 0.7688 (mp-120) cc_final: 0.6984 (tm-30) REVERT: B 285 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: B 463 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7081 (pp30) REVERT: B 582 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: B 603 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7938 (mm-30) outliers start: 10 outliers final: 2 residues processed: 130 average time/residue: 1.4380 time to fit residues: 199.5015 Evaluate side-chains 132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS 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 16 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.142994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112945 restraints weight = 8204.770| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.06 r_work: 0.2973 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9822 Z= 0.169 Angle : 0.545 7.656 13168 Z= 0.277 Chirality : 0.042 0.147 1398 Planarity : 0.004 0.037 1578 Dihedral : 18.360 108.203 1874 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.07 % Allowed : 13.25 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.25), residues: 1096 helix: 1.52 (0.19), residues: 764 sheet: -3.01 (0.89), residues: 20 loop : 1.26 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.003 0.001 HIS A 312 PHE 0.012 0.001 PHE B 209 TYR 0.009 0.001 TYR A 495 ARG 0.002 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8041.53 seconds wall clock time: 142 minutes 28.21 seconds (8548.21 seconds total)