Starting phenix.real_space_refine on Sun Jun 8 16:55:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teh_41186/06_2025/8teh_41186.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teh_41186/06_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_41186/06_2025/8teh_41186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teh_41186/06_2025/8teh_41186.map" model { file = "/net/cci-nas-00/data/ceres_data/8teh_41186/06_2025/8teh_41186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teh_41186/06_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-5710/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: 6.79, per 1000 atoms: 0.69 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: 2.86 Conformation dependent library (CDL) restraints added in 1.0 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: 1.10 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: 3.07 Time building geometry restraints manager: 3.17 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: 0.010 Normalize map: mean=0, sd=1: 2.230 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.300 Find NCS groups from input model: 0.610 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: 0.010 Load rotamer database and sin/cos tables:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.340 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13611 ( 562) hydrogen bonds : angle 5.48904 ( 1608) covalent geometry : bond 0.02622 ( 9822) covalent geometry : angle 0.66707 (13168) 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 : 1.131 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: 1.6321 time to fit residues: 213.2588 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 : 1.050 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.111114 restraints weight = 7906.034| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.05 r_work: 0.2969 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 9824 Z= 0.156 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 Details of bonding type rmsd hydrogen bonds : bond 0.06191 ( 562) hydrogen bonds : angle 4.86746 ( 1608) covalent geometry : bond 0.00316 ( 9822) covalent geometry : angle 0.61356 (13168) Misc. bond : bond 0.00247 ( 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 140 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.023 Fit side-chains REVERT: A 187 GLN cc_start: 0.7173 (mt0) cc_final: 0.6839 (mm-40) REVERT: A 220 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7883 (mppt) REVERT: A 285 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 463 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7395 (pp30) REVERT: A 517 PHE cc_start: 0.7897 (m-80) cc_final: 0.7634 (m-80) REVERT: A 582 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: A 603 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8052 (mm-30) REVERT: B 187 GLN cc_start: 0.7190 (mt0) cc_final: 0.6851 (mm-40) REVERT: B 220 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7877 (mppt) REVERT: B 285 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: B 463 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7385 (pp30) REVERT: B 517 PHE cc_start: 0.7878 (m-80) cc_final: 0.7620 (m-80) REVERT: B 582 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: B 584 LEU cc_start: 0.8307 (mt) cc_final: 0.8097 (mm) REVERT: B 603 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7952 (mm-30) outliers start: 13 outliers final: 0 residues processed: 133 average time/residue: 1.9436 time to fit residues: 273.3150 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 : 0.989 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.142600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110375 restraints weight = 8080.018| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.05 r_work: 0.2959 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1678 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= 0.141 Angle : 0.565 7.593 13168 Z= 0.287 Chirality : 0.043 0.158 1398 Planarity : 0.004 0.036 1578 Dihedral : 22.029 116.741 1874 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.71 % Allowed : 10.90 % 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 (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: 1.79 (0.25), residues: 1096 helix: 1.40 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.98 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE B 534 TYR 0.010 0.002 TYR A 495 ARG 0.004 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.05969 ( 562) hydrogen bonds : angle 4.76350 ( 1608) covalent geometry : bond 0.00291 ( 9822) covalent geometry : angle 0.56509 (13168) Misc. bond : bond 0.00046 ( 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 140 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.038 Fit side-chains REVERT: A 20 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7571 (mmm) REVERT: A 119 ASP cc_start: 0.7897 (m-30) cc_final: 0.7597 (m-30) REVERT: A 187 GLN cc_start: 0.7264 (mt0) cc_final: 0.6919 (mm-40) REVERT: A 285 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 463 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7433 (pp30) REVERT: A 541 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7500 (ttpt) REVERT: A 582 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: A 603 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: B 20 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7568 (mmm) REVERT: B 119 ASP cc_start: 0.7753 (m-30) cc_final: 0.7530 (m-30) REVERT: B 187 GLN cc_start: 0.7270 (mt0) cc_final: 0.6916 (mm-40) REVERT: B 285 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: B 463 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7419 (pp30) REVERT: B 541 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7512 (ttpt) REVERT: B 582 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: B 584 LEU cc_start: 0.8440 (mt) cc_final: 0.8236 (mm) REVERT: B 603 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7925 (mm-30) outliers start: 16 outliers final: 2 residues processed: 131 average time/residue: 1.4875 time to fit residues: 206.9003 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 : 0.963 ------------------------------------------------------------------------------- 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: 0.4980 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.0040 chunk 91 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.145743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.113829 restraints weight = 8038.717| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.05 r_work: 0.3014 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1781 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 : 0.498 7.260 13168 Z= 0.252 Chirality : 0.040 0.142 1398 Planarity : 0.004 0.030 1578 Dihedral : 20.965 110.989 1874 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.07 % Allowed : 12.29 % 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: 2.09 (0.25), residues: 1096 helix: 1.59 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 1.19 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.003 0.001 HIS B 644 PHE 0.014 0.001 PHE A 534 TYR 0.007 0.001 TYR B 495 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 562) hydrogen bonds : angle 4.50293 ( 1608) covalent geometry : bond 0.00221 ( 9822) covalent geometry : angle 0.49802 (13168) Misc. bond : bond 0.00004 ( 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 132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.122 Fit side-chains REVERT: A 119 ASP cc_start: 0.7822 (m-30) cc_final: 0.7550 (m-30) REVERT: A 187 GLN cc_start: 0.7248 (mt0) cc_final: 0.6883 (mm-40) REVERT: A 285 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: A 298 PHE cc_start: 0.7986 (t80) cc_final: 0.7763 (t80) REVERT: A 463 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7223 (pp30) REVERT: A 582 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: B 119 ASP cc_start: 0.7714 (m-30) cc_final: 0.7514 (m-30) REVERT: B 187 GLN cc_start: 0.7264 (mt0) cc_final: 0.6894 (mm-40) REVERT: B 285 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: B 463 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7220 (pp30) REVERT: B 582 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7938 (mp10) outliers start: 10 outliers final: 0 residues processed: 128 average time/residue: 1.3534 time to fit residues: 185.3468 Evaluate side-chains 125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 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 108 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.143315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110984 restraints weight = 8048.203| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.06 r_work: 0.2967 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1882 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= 0.131 Angle : 0.538 7.447 13168 Z= 0.274 Chirality : 0.042 0.149 1398 Planarity : 0.004 0.033 1578 Dihedral : 20.497 103.333 1874 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.24 % Allowed : 11.22 % 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 (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: 1.90 (0.25), residues: 1096 helix: 1.49 (0.19), residues: 760 sheet: -2.48 (0.95), residues: 20 loop : 1.25 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.003 0.001 HIS B 644 PHE 0.012 0.001 PHE A 209 TYR 0.008 0.001 TYR B 495 ARG 0.002 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.05645 ( 562) hydrogen bonds : angle 4.61044 ( 1608) covalent geometry : bond 0.00264 ( 9822) covalent geometry : angle 0.53847 (13168) Misc. bond : bond 0.00021 ( 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 138 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.317 Fit side-chains REVERT: A 20 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7518 (mmm) REVERT: A 119 ASP cc_start: 0.7924 (m-30) cc_final: 0.7654 (m-30) REVERT: A 187 GLN cc_start: 0.7284 (mt0) cc_final: 0.6870 (mm-40) REVERT: A 285 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: A 298 PHE cc_start: 0.8038 (t80) cc_final: 0.7814 (t80) REVERT: A 463 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7424 (pp30) REVERT: A 541 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7511 (ttpt) REVERT: A 582 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: B 20 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7530 (mmm) REVERT: B 187 GLN cc_start: 0.7292 (mt0) cc_final: 0.6880 (mm-40) REVERT: B 285 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: B 463 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7426 (pp30) REVERT: B 541 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7523 (ttpt) REVERT: B 582 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: B 603 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7971 (mm-30) outliers start: 21 outliers final: 3 residues processed: 129 average time/residue: 1.5534 time to fit residues: 213.0164 Evaluate side-chains 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 161 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 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: 2.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 38 optimal weight: 5.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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 = 0.141751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.110707 restraints weight = 8132.372| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.12 r_work: 0.2944 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9824 Z= 0.152 Angle : 0.584 7.988 13168 Z= 0.297 Chirality : 0.044 0.156 1398 Planarity : 0.004 0.035 1578 Dihedral : 20.550 108.555 1874 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.35 % Allowed : 11.43 % 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 (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: 1.38 (0.19), residues: 748 sheet: -2.23 (0.95), residues: 20 loop : 1.06 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 247 HIS 0.004 0.001 HIS B 644 PHE 0.014 0.002 PHE A 209 TYR 0.010 0.002 TYR B 495 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.06304 ( 562) hydrogen bonds : angle 4.76694 ( 1608) covalent geometry : bond 0.00317 ( 9822) covalent geometry : angle 0.58387 (13168) 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 137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.990 Fit side-chains REVERT: A 20 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7523 (mmm) REVERT: A 225 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8057 (ptt180) REVERT: A 285 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: A 463 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7471 (pp30) REVERT: A 541 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7572 (ttpt) REVERT: A 633 GLU cc_start: 0.7765 (pt0) cc_final: 0.7561 (pt0) REVERT: B 20 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7503 (mmm) REVERT: B 285 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 463 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7475 (pp30) REVERT: B 541 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7585 (ttpt) REVERT: B 582 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: B 603 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8008 (mm-30) REVERT: B 633 GLU cc_start: 0.7769 (pt0) cc_final: 0.7564 (pt0) outliers start: 22 outliers final: 2 residues processed: 128 average time/residue: 1.6812 time to fit residues: 228.8455 Evaluate side-chains 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 225 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.0470 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.144370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114615 restraints weight = 8233.734| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.10 r_work: 0.3009 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1988 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= 0.119 Angle : 0.516 7.535 13168 Z= 0.262 Chirality : 0.041 0.145 1398 Planarity : 0.004 0.033 1578 Dihedral : 19.844 107.482 1874 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.60 % Allowed : 11.65 % Favored : 86.75 % 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: 1.96 (0.25), residues: 1096 helix: 1.53 (0.19), residues: 762 sheet: -2.07 (0.93), residues: 20 loop : 1.25 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 247 HIS 0.002 0.001 HIS B 644 PHE 0.012 0.001 PHE A 534 TYR 0.008 0.001 TYR B 495 ARG 0.002 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 562) hydrogen bonds : angle 4.52953 ( 1608) covalent geometry : bond 0.00236 ( 9822) covalent geometry : angle 0.51642 (13168) Misc. bond : bond 0.00009 ( 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 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.128 Fit side-chains REVERT: A 20 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7463 (mmm) REVERT: A 187 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6848 (mm-40) REVERT: A 285 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: A 463 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7349 (pp30) REVERT: B 187 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6868 (mm-40) REVERT: B 285 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: B 463 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7359 (pp30) REVERT: B 582 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: B 603 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7966 (mm-30) outliers start: 15 outliers final: 4 residues processed: 125 average time/residue: 2.0680 time to fit residues: 278.6155 Evaluate side-chains 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 161 LEU 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 161 LEU 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 582 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 71 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.145754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.113854 restraints weight = 8254.419| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.13 r_work: 0.3019 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2067 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= 0.112 Angle : 0.498 7.352 13168 Z= 0.251 Chirality : 0.040 0.142 1398 Planarity : 0.004 0.033 1578 Dihedral : 18.847 105.914 1874 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.71 % Allowed : 12.50 % 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 (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: 2.12 (0.25), residues: 1096 helix: 1.68 (0.19), residues: 762 sheet: -2.66 (0.83), residues: 20 loop : 1.30 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.002 0.001 HIS B 644 PHE 0.013 0.001 PHE A 534 TYR 0.007 0.001 TYR B 495 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 562) hydrogen bonds : angle 4.38109 ( 1608) covalent geometry : bond 0.00219 ( 9822) covalent geometry : angle 0.49755 (13168) Misc. bond : bond 0.00008 ( 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 140 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.023 Fit side-chains REVERT: A 20 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7519 (mmm) REVERT: A 187 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6916 (mm-40) REVERT: A 285 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: A 463 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7276 (pp30) REVERT: B 20 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7516 (mmm) REVERT: B 24 GLN cc_start: 0.7751 (mp-120) cc_final: 0.7049 (tm-30) REVERT: B 187 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6922 (mm-40) REVERT: B 285 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: B 463 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7268 (pp30) REVERT: B 582 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7889 (mp10) outliers start: 16 outliers final: 4 residues processed: 131 average time/residue: 1.4387 time to fit residues: 201.1664 Evaluate side-chains 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 161 LEU 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 161 LEU 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 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: 0.3980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3600 r_free = 0.3600 target = 0.145039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115417 restraints weight = 8230.965| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.10 r_work: 0.3024 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2091 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= 0.115 Angle : 0.507 7.397 13168 Z= 0.256 Chirality : 0.041 0.143 1398 Planarity : 0.004 0.034 1578 Dihedral : 18.489 106.860 1874 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.60 % Allowed : 12.82 % Favored : 85.58 % 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: 2.09 (0.25), residues: 1096 helix: 1.65 (0.19), residues: 764 sheet: -2.91 (0.80), residues: 20 loop : 1.32 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 247 HIS 0.003 0.001 HIS B 644 PHE 0.011 0.001 PHE A 534 TYR 0.007 0.001 TYR A 495 ARG 0.002 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 562) hydrogen bonds : angle 4.41741 ( 1608) covalent geometry : bond 0.00225 ( 9822) covalent geometry : angle 0.50742 (13168) Misc. bond : bond 0.00016 ( 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 136 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.997 Fit side-chains REVERT: A 187 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6859 (mm-40) REVERT: A 285 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: A 463 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7261 (pp30) REVERT: B 187 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6865 (mm-40) REVERT: B 285 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: B 463 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7396 (pp30) REVERT: B 603 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7931 (mm-30) outliers start: 15 outliers final: 4 residues processed: 127 average time/residue: 1.5460 time to fit residues: 209.7355 Evaluate side-chains 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 161 LEU 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 161 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.144671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.112387 restraints weight = 8228.798| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.16 r_work: 0.3000 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2143 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= 0.118 Angle : 0.513 7.541 13168 Z= 0.259 Chirality : 0.041 0.145 1398 Planarity : 0.004 0.034 1578 Dihedral : 18.118 107.668 1874 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.07 % Allowed : 13.46 % Favored : 85.47 % 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: 2.10 (0.25), residues: 1096 helix: 1.71 (0.19), residues: 752 sheet: -2.88 (0.81), residues: 20 loop : 1.18 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.002 0.001 HIS A 644 PHE 0.011 0.001 PHE A 534 TYR 0.008 0.001 TYR A 495 ARG 0.003 0.000 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 562) hydrogen bonds : angle 4.41898 ( 1608) covalent geometry : bond 0.00234 ( 9822) covalent geometry : angle 0.51259 (13168) Misc. bond : bond 0.00019 ( 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 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.096 Fit side-chains REVERT: A 285 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 463 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7418 (pp30) REVERT: B 285 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: B 463 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7433 (pp30) REVERT: B 603 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7955 (mm-30) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 1.6617 time to fit residues: 220.0333 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 : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 161 LEU 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 161 LEU 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 1 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.112855 restraints weight = 8200.857| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.12 r_work: 0.2997 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2144 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= 0.126 Angle : 0.532 7.777 13168 Z= 0.270 Chirality : 0.041 0.148 1398 Planarity : 0.004 0.034 1578 Dihedral : 18.083 109.579 1874 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.07 % Allowed : 13.46 % Favored : 85.47 % 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: 1.99 (0.25), residues: 1096 helix: 1.62 (0.19), residues: 752 sheet: -2.84 (0.81), residues: 20 loop : 1.15 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 247 HIS 0.002 0.001 HIS B 312 PHE 0.011 0.001 PHE A 534 TYR 0.009 0.001 TYR A 495 ARG 0.002 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.05421 ( 562) hydrogen bonds : angle 4.49316 ( 1608) covalent geometry : bond 0.00252 ( 9822) covalent geometry : angle 0.53222 (13168) Misc. bond : bond 0.00017 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8953.23 seconds wall clock time: 156 minutes 50.45 seconds (9410.45 seconds total)