Starting phenix.real_space_refine on Fri Feb 14 05:09:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tei_41187/02_2025/8tei_41187.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tei_41187/02_2025/8tei_41187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tei_41187/02_2025/8tei_41187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tei_41187/02_2025/8tei_41187.map" model { file = "/net/cci-nas-00/data/ceres_data/8tei_41187/02_2025/8tei_41187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tei_41187/02_2025/8tei_41187.cif" } resolution = 2.58 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= 0.003 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 34 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: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 427 Unusual residues: {'POV': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 427 Unusual residues: {'POV': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 23 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: 6.26, per 1000 atoms: 0.64 Number of scatterers: 9816 At special positions: 0 Unit cell: (92.13, 118.69, 86.32, 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=0, symmetry=0 Time building additional restraints: 3.67 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: 66 helices and 6 sheets defined 77.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.756A pdb=" N MET A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.544A 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: 3.837A 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 Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.556A pdb=" N ILE A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 4.916A 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: 3.531A pdb=" N SER A 223 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 252 removed outlier: 6.536A 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: 4.612A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.620A 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: 3.561A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.724A 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: 3.601A pdb=" N LEU A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.141A 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: 3.709A 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: 3.815A 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 589 removed outlier: 3.567A pdb=" N MET A 573 " --> pdb=" O MET A 569 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 4.417A pdb=" N LEU A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Proline residue: A 586 - end of helix Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.768A pdb=" N GLU A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 635 removed outlier: 3.738A pdb=" N GLU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.756A pdb=" N MET B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 removed outlier: 3.544A 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: 3.837A 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 Processing helix chain 'B' and resid 120 through 142 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.556A pdb=" N ILE B 147 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.916A 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: 3.531A pdb=" N SER B 223 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 6.535A 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: 4.612A pdb=" N GLY B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.621A 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: 3.562A pdb=" N MET B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.724A 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: 3.602A pdb=" N LEU B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 4.140A 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: 3.709A 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: 3.816A 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 589 removed outlier: 3.568A pdb=" N MET B 573 " --> pdb=" O MET B 569 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 577 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix removed outlier: 4.417A pdb=" N LEU B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) Proline residue: B 586 - end of helix Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 609 through 615 removed outlier: 3.768A pdb=" N GLU B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 635 removed outlier: 3.738A 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: 6.045A 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 371 556 hydrogen bonds defined for protein. 1596 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: 3.05 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.62: 9686 1.62 - 2.03: 134 2.03 - 2.44: 0 2.44 - 2.86: 0 2.86 - 3.27: 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 3.272 -1.748 2.00e-02 2.50e+03 7.64e+03 bond pdb="C214 POV B 811 " pdb="C215 POV B 811 " ideal model delta sigma weight residual 1.524 3.271 -1.747 2.00e-02 2.50e+03 7.63e+03 bond pdb=" C29 POV A 810 " pdb="C210 POV A 810 " ideal model delta sigma weight residual 1.333 1.526 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" C29 POV B 805 " pdb="C210 POV B 805 " ideal model delta sigma weight residual 1.333 1.525 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" C29 POV A 801 " pdb="C210 POV A 801 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.16e+01 ... (remaining 9817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 13082 3.08 - 6.16: 70 6.16 - 9.24: 0 9.24 - 12.32: 4 12.32 - 15.40: 12 Bond angle restraints: 13168 Sorted by residual: angle pdb="C214 POV B 811 " pdb="C215 POV B 811 " pdb="C216 POV B 811 " ideal model delta sigma weight residual 113.14 128.54 -15.40 3.00e+00 1.11e-01 2.63e+01 angle pdb="C214 POV A 804 " pdb="C215 POV A 804 " pdb="C216 POV A 804 " ideal model delta sigma weight residual 113.14 128.52 -15.38 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C28 POV B 805 " pdb=" C29 POV B 805 " pdb="C210 POV B 805 " ideal model delta sigma weight residual 127.79 113.70 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C28 POV A 810 " pdb=" C29 POV A 810 " pdb="C210 POV A 810 " ideal model delta sigma weight residual 127.79 113.74 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C28 POV B 808 " pdb=" C29 POV B 808 " pdb="C210 POV B 808 " ideal model delta sigma weight residual 127.79 113.91 13.88 3.00e+00 1.11e-01 2.14e+01 ... (remaining 13163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 5553 34.79 - 69.58: 355 69.58 - 104.37: 50 104.37 - 139.16: 2 139.16 - 173.95: 4 Dihedral angle restraints: 5964 sinusoidal: 2778 harmonic: 3186 Sorted by residual: dihedral pdb=" C29 POV B 805 " pdb="C210 POV B 805 " pdb="C211 POV B 805 " pdb="C212 POV B 805 " ideal model delta sinusoidal sigma weight residual 112.25 -73.80 -173.95 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV A 810 " pdb="C210 POV A 810 " pdb="C211 POV A 810 " pdb="C212 POV A 810 " ideal model delta sinusoidal sigma weight residual 112.25 -73.89 -173.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C27 POV B 805 " pdb=" C28 POV B 805 " pdb=" C29 POV B 805 " pdb="C210 POV B 805 " ideal model delta sinusoidal sigma weight residual 127.48 -81.43 -151.09 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 5961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 914 0.028 - 0.057: 309 0.057 - 0.085: 103 0.085 - 0.113: 60 0.113 - 0.141: 12 Chirality restraints: 1398 Sorted by residual: 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 5.00e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 181 " pdb=" N ILE B 181 " pdb=" C ILE B 181 " pdb=" CB ILE B 181 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1395 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 808 " -0.146 2.00e-02 2.50e+03 3.18e-01 1.01e+03 pdb=" C29 POV B 808 " 0.417 2.00e-02 2.50e+03 pdb="C210 POV B 808 " -0.428 2.00e-02 2.50e+03 pdb="C211 POV B 808 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 801 " 0.146 2.00e-02 2.50e+03 3.17e-01 1.01e+03 pdb=" C29 POV A 801 " -0.417 2.00e-02 2.50e+03 pdb="C210 POV A 801 " 0.428 2.00e-02 2.50e+03 pdb="C211 POV A 801 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B 805 " -0.131 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C29 POV B 805 " 0.295 2.00e-02 2.50e+03 pdb="C210 POV B 805 " -0.298 2.00e-02 2.50e+03 pdb="C211 POV B 805 " 0.135 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 158 2.60 - 3.18: 8359 3.18 - 3.75: 15476 3.75 - 4.33: 23093 4.33 - 4.90: 36940 Nonbonded interactions: 84026 Sorted by model distance: nonbonded pdb=" O PHE B 558 " pdb=" OG1 THR B 561 " model vdw 2.028 3.040 nonbonded pdb=" O PHE A 558 " pdb=" OG1 THR A 561 " model vdw 2.028 3.040 nonbonded pdb=" OD2 ASP B 311 " pdb=" O HOH B 901 " model vdw 2.053 3.040 nonbonded pdb=" OD2 ASP A 311 " pdb=" O HOH A 901 " model vdw 2.053 3.040 nonbonded pdb=" OH TYR A 495 " pdb=" O HOH A 902 " model vdw 2.100 3.040 ... (remaining 84021 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: 0.04 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 C22 or nam \ e 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)) or (resid 806 and (name C1 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 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 O21 or name O22 or name O31 or name O32 or name P or name C310 or name C311 \ )) or resid 807 or (resid 808 and (name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27)) or (resid 809 and (name C1 or name C2 or n \ ame 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 resid 810 through 811 or (resid 812 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 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 name C3 or name C31 or name C32 or name C33 or nam \ e 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 O3 \ 2 or name P or name C210 or name C211 or name C212 or name C213 or name C310 or \ name C311 or name C312 or name C313 or name C314 or name C315 or name C316)))) 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 or (resid 805 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)) or (resid 806 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 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 O21 or name O22 or name O31 \ or name O32 or name P or name C310 or name C311)) or (resid 807 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 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 name C3 or name C31 or name C32 or name C33 or nam \ e 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 O3 \ 2 or name P or name C210 or name C211 or name C310)) or (resid 808 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27)) or (r \ esid 809 and (name C1 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 (resid 810 and \ (name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C210 or name C211 or name C212 or name C213 or name C214 \ or name C215 or name C216)) or (resid 811 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 name C22 \ or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 o \ r name O31 or name O32 or name P or name C310 or name C311)) or resid 812)) } 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: 1.980 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.140 Find NCS groups from input model: 0.620 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:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.025 1.748 9822 Z= 1.624 Angle : 0.688 15.396 13168 Z= 0.304 Chirality : 0.037 0.141 1398 Planarity : 0.014 0.318 1578 Dihedral : 21.719 173.947 3916 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 15.28 % Favored : 84.72 % 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: 2.53 (0.26), residues: 1096 helix: 1.98 (0.20), residues: 750 sheet: None (None), residues: 0 loop : 1.20 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 247 HIS 0.002 0.001 HIS B 333 PHE 0.009 0.001 PHE A 588 TYR 0.007 0.001 TYR B 495 ARG 0.003 0.000 ARG A 327 *********************** 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 115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.925 Fit side-chains REVERT: A 80 MET cc_start: 0.8807 (mtp) cc_final: 0.8566 (mtm) REVERT: A 575 MET cc_start: 0.7642 (ttt) cc_final: 0.6752 (tpt) REVERT: B 80 MET cc_start: 0.8810 (mtp) cc_final: 0.8553 (mtm) REVERT: B 575 MET cc_start: 0.7614 (ttt) cc_final: 0.6736 (tpt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 1.3626 time to fit residues: 167.6682 Evaluate side-chains 107 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 595 GLN B 13 ASN B 595 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.111036 restraints weight = 9498.151| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.34 r_work: 0.2911 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9822 Z= 0.194 Angle : 0.562 6.595 13168 Z= 0.280 Chirality : 0.042 0.165 1398 Planarity : 0.004 0.037 1578 Dihedral : 21.365 131.668 1874 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.24 % Allowed : 12.82 % Favored : 84.94 % 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: 2.22 (0.26), residues: 1096 helix: 1.60 (0.19), residues: 784 sheet: -1.82 (0.94), residues: 20 loop : 1.71 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.003 0.001 HIS B 312 PHE 0.012 0.001 PHE A 298 TYR 0.006 0.001 TYR A 22 ARG 0.003 0.000 ARG B 180 *********************** 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 143 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.059 Fit side-chains REVERT: A 80 MET cc_start: 0.9018 (mtp) cc_final: 0.8770 (mtm) REVERT: A 459 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: A 575 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.6725 (tpt) REVERT: A 595 GLN cc_start: 0.7427 (tp-100) cc_final: 0.6832 (tp40) REVERT: A 603 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: B 459 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: B 595 GLN cc_start: 0.7406 (tp-100) cc_final: 0.6795 (tp40) REVERT: B 603 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7430 (mp0) outliers start: 21 outliers final: 7 residues processed: 137 average time/residue: 1.6459 time to fit residues: 238.5774 Evaluate side-chains 120 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 575 MET 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: 7.9990 chunk 52 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 0.0070 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 88 GLN A 170 GLN A 320 GLN B 13 ASN B 88 GLN B 170 GLN B 320 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.106212 restraints weight = 9646.887| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.36 r_work: 0.2852 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2020 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= 0.197 Angle : 0.554 6.872 13168 Z= 0.278 Chirality : 0.043 0.168 1398 Planarity : 0.004 0.040 1578 Dihedral : 20.338 123.119 1874 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.53 % Allowed : 11.86 % Favored : 84.62 % 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: 2.04 (0.25), residues: 1096 helix: 1.50 (0.19), residues: 770 sheet: -2.00 (0.86), residues: 20 loop : 1.54 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.004 0.001 HIS B 364 PHE 0.013 0.001 PHE A 534 TYR 0.008 0.001 TYR A 22 ARG 0.003 0.001 ARG B 180 *********************** 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 158 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.178 Fit side-chains REVERT: A 9 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: A 370 THR cc_start: 0.8499 (p) cc_final: 0.8112 (t) REVERT: A 459 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: A 463 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7500 (pp30) REVERT: A 582 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: A 583 TYR cc_start: 0.7987 (m-80) cc_final: 0.7753 (m-80) REVERT: A 595 GLN cc_start: 0.7492 (tp-100) cc_final: 0.6907 (tp40) REVERT: A 601 GLU cc_start: 0.7927 (mp0) cc_final: 0.6908 (mp0) REVERT: A 603 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: B 9 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: B 285 GLU cc_start: 0.7997 (mp0) cc_final: 0.7675 (mp0) REVERT: B 370 THR cc_start: 0.8495 (p) cc_final: 0.8109 (t) REVERT: B 463 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7475 (pp30) REVERT: B 582 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: B 583 TYR cc_start: 0.8002 (m-80) cc_final: 0.7754 (m-80) REVERT: B 595 GLN cc_start: 0.7493 (tp-100) cc_final: 0.6905 (tp40) outliers start: 33 outliers final: 7 residues processed: 143 average time/residue: 1.6283 time to fit residues: 247.2275 Evaluate side-chains 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 582 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 chunk 91 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN B 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104468 restraints weight = 9532.046| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.36 r_work: 0.2824 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2394 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= 0.200 Angle : 0.545 6.969 13168 Z= 0.274 Chirality : 0.043 0.167 1398 Planarity : 0.004 0.041 1578 Dihedral : 19.775 103.679 1874 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.42 % Allowed : 12.82 % Favored : 83.76 % 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: 1.47 (0.19), residues: 770 sheet: -2.69 (0.81), residues: 20 loop : 1.49 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 531 PHE 0.016 0.002 PHE B 534 TYR 0.013 0.001 TYR A 293 ARG 0.004 0.000 ARG B 180 *********************** 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 163 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.042 Fit side-chains REVERT: A 9 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: A 285 GLU cc_start: 0.8057 (mp0) cc_final: 0.7764 (mp0) REVERT: A 370 THR cc_start: 0.8503 (p) cc_final: 0.8135 (t) REVERT: A 463 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7932 (pp30) REVERT: A 582 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7250 (mm-40) REVERT: A 595 GLN cc_start: 0.7496 (tp-100) cc_final: 0.6883 (tp40) REVERT: A 601 GLU cc_start: 0.7954 (mp0) cc_final: 0.7319 (mp0) REVERT: B 9 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: B 285 GLU cc_start: 0.8044 (mp0) cc_final: 0.7763 (mp0) REVERT: B 370 THR cc_start: 0.8493 (p) cc_final: 0.8122 (t) REVERT: B 459 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: B 463 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7973 (pp30) REVERT: B 582 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7281 (mm-40) REVERT: B 595 GLN cc_start: 0.7505 (tp-100) cc_final: 0.6890 (tp40) REVERT: B 601 GLU cc_start: 0.7981 (mp0) cc_final: 0.7287 (mp0) outliers start: 32 outliers final: 7 residues processed: 152 average time/residue: 1.6994 time to fit residues: 273.7722 Evaluate side-chains 141 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 575 MET 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: 5.9990 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 270 ASN B 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.101294 restraints weight = 9610.016| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.37 r_work: 0.2773 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9822 Z= 0.296 Angle : 0.625 7.263 13168 Z= 0.313 Chirality : 0.046 0.176 1398 Planarity : 0.005 0.047 1578 Dihedral : 19.908 96.546 1874 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.10 % Allowed : 13.89 % Favored : 83.01 % 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: 1.69 (0.25), residues: 1096 helix: 1.25 (0.18), residues: 766 sheet: None (None), residues: 0 loop : 1.14 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.002 PHE B 534 TYR 0.015 0.002 TYR A 293 ARG 0.003 0.000 ARG A 180 *********************** 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 158 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.059 Fit side-chains REVERT: A 9 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: A 285 GLU cc_start: 0.8117 (mp0) cc_final: 0.7817 (mp0) REVERT: A 370 THR cc_start: 0.8513 (p) cc_final: 0.8128 (t) REVERT: A 459 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: A 463 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7945 (pp30) REVERT: A 511 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: A 582 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: A 595 GLN cc_start: 0.7576 (tp-100) cc_final: 0.6958 (tp40) REVERT: A 601 GLU cc_start: 0.7993 (mp0) cc_final: 0.7350 (mp0) REVERT: B 9 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: B 285 GLU cc_start: 0.8054 (mp0) cc_final: 0.7756 (mp0) REVERT: B 370 THR cc_start: 0.8513 (p) cc_final: 0.8125 (t) REVERT: B 459 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: B 463 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.7984 (pp30) REVERT: B 511 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: B 582 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: B 595 GLN cc_start: 0.7571 (tp-100) cc_final: 0.6954 (tp40) REVERT: B 601 GLU cc_start: 0.7977 (mp0) cc_final: 0.6895 (mp0) REVERT: B 603 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7359 (mp0) outliers start: 29 outliers final: 11 residues processed: 145 average time/residue: 1.5328 time to fit residues: 235.9949 Evaluate side-chains 146 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 575 MET 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: 8.9990 chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 270 ASN A 333 HIS B 13 ASN B 333 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106764 restraints weight = 9633.035| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.35 r_work: 0.2835 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9822 Z= 0.172 Angle : 0.517 6.957 13168 Z= 0.261 Chirality : 0.041 0.164 1398 Planarity : 0.004 0.042 1578 Dihedral : 18.826 93.070 1874 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.24 % Allowed : 14.96 % Favored : 82.80 % 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: 1.94 (0.25), residues: 1096 helix: 1.49 (0.19), residues: 766 sheet: -2.97 (0.89), residues: 20 loop : 1.38 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.015 0.001 PHE A 534 TYR 0.009 0.001 TYR A 293 ARG 0.002 0.000 ARG A 180 *********************** 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 147 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.059 Fit side-chains REVERT: A 9 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: A 285 GLU cc_start: 0.8074 (mp0) cc_final: 0.7799 (mp0) REVERT: A 370 THR cc_start: 0.8480 (p) cc_final: 0.8131 (t) REVERT: A 459 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: A 463 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7659 (pp30) REVERT: A 511 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: A 582 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7287 (mm-40) REVERT: A 595 GLN cc_start: 0.7521 (tp-100) cc_final: 0.6910 (tp40) REVERT: A 601 GLU cc_start: 0.7975 (mp0) cc_final: 0.7341 (mp0) REVERT: B 9 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: B 285 GLU cc_start: 0.7991 (mp0) cc_final: 0.7704 (mp0) REVERT: B 370 THR cc_start: 0.8538 (p) cc_final: 0.8178 (t) REVERT: B 459 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: B 463 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7677 (pp30) REVERT: B 511 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: B 582 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7291 (mm-40) REVERT: B 595 GLN cc_start: 0.7510 (tp-100) cc_final: 0.6902 (tp40) REVERT: B 601 GLU cc_start: 0.7918 (mp0) cc_final: 0.7266 (mp0) outliers start: 21 outliers final: 6 residues processed: 137 average time/residue: 1.5466 time to fit residues: 224.9371 Evaluate side-chains 139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 582 GLN 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: 7.9990 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 270 ASN B 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.102492 restraints weight = 9700.929| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.38 r_work: 0.2800 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2789 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= 0.217 Angle : 0.564 6.919 13168 Z= 0.283 Chirality : 0.043 0.166 1398 Planarity : 0.005 0.043 1578 Dihedral : 18.596 94.940 1874 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.67 % Allowed : 14.64 % Favored : 82.69 % 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: 1.85 (0.25), residues: 1096 helix: 1.41 (0.19), residues: 768 sheet: -3.02 (0.90), residues: 20 loop : 1.41 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS B 364 PHE 0.014 0.002 PHE A 534 TYR 0.008 0.001 TYR B 495 ARG 0.002 0.000 ARG B 180 *********************** 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 152 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.997 Fit side-chains REVERT: A 9 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: A 284 LYS cc_start: 0.7807 (ttmp) cc_final: 0.7444 (tttm) REVERT: A 285 GLU cc_start: 0.8124 (mp0) cc_final: 0.7839 (mp0) REVERT: A 370 THR cc_start: 0.8500 (p) cc_final: 0.8150 (t) REVERT: A 459 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 463 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7823 (pp30) REVERT: A 511 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: A 582 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: A 595 GLN cc_start: 0.7571 (tp-100) cc_final: 0.6958 (tp40) REVERT: A 601 GLU cc_start: 0.8009 (mp0) cc_final: 0.7356 (mp0) REVERT: B 9 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: B 284 LYS cc_start: 0.7808 (ttmp) cc_final: 0.7455 (tttm) REVERT: B 285 GLU cc_start: 0.8118 (mp0) cc_final: 0.7841 (mp0) REVERT: B 370 THR cc_start: 0.8514 (p) cc_final: 0.8164 (t) REVERT: B 459 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: B 463 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7804 (pp30) REVERT: B 511 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: B 582 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: B 595 GLN cc_start: 0.7555 (tp-100) cc_final: 0.6945 (tp40) REVERT: B 601 GLU cc_start: 0.7932 (mp0) cc_final: 0.7285 (mp0) outliers start: 25 outliers final: 8 residues processed: 141 average time/residue: 1.5671 time to fit residues: 234.2598 Evaluate side-chains 144 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 575 MET 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: 0.8980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 270 ASN B 13 ASN B 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107318 restraints weight = 9676.192| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.36 r_work: 0.2847 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9822 Z= 0.157 Angle : 0.505 6.805 13168 Z= 0.255 Chirality : 0.041 0.158 1398 Planarity : 0.004 0.040 1578 Dihedral : 17.935 92.007 1874 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.71 % Allowed : 15.60 % Favored : 82.69 % 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: 1.60 (0.19), residues: 766 sheet: -3.21 (0.87), residues: 20 loop : 1.51 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 247 HIS 0.002 0.001 HIS B 312 PHE 0.015 0.001 PHE A 534 TYR 0.006 0.001 TYR B 309 ARG 0.002 0.000 ARG A 180 *********************** 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 142 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.020 Fit side-chains REVERT: A 9 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: A 284 LYS cc_start: 0.7842 (ttmp) cc_final: 0.7488 (tttm) REVERT: A 285 GLU cc_start: 0.8041 (mp0) cc_final: 0.7750 (mp0) REVERT: A 370 THR cc_start: 0.8530 (p) cc_final: 0.8192 (t) REVERT: A 459 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 463 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7509 (pp30) REVERT: A 511 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: A 575 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.6608 (tpt) REVERT: A 595 GLN cc_start: 0.7507 (tp-100) cc_final: 0.6911 (tp40) REVERT: A 601 GLU cc_start: 0.7969 (mp0) cc_final: 0.7326 (mp0) REVERT: B 9 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: B 284 LYS cc_start: 0.7828 (ttmp) cc_final: 0.7475 (tttm) REVERT: B 285 GLU cc_start: 0.8007 (mp0) cc_final: 0.7715 (mp0) REVERT: B 370 THR cc_start: 0.8563 (p) cc_final: 0.8218 (t) REVERT: B 459 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: B 463 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7497 (pp30) REVERT: B 511 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: B 575 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6614 (tpt) REVERT: B 595 GLN cc_start: 0.7496 (tp-100) cc_final: 0.6901 (tp40) REVERT: B 601 GLU cc_start: 0.7906 (mp0) cc_final: 0.7227 (mp0) outliers start: 16 outliers final: 4 residues processed: 134 average time/residue: 1.5835 time to fit residues: 224.9397 Evaluate side-chains 139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 575 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 270 ASN B 13 ASN B 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102448 restraints weight = 9538.200| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.42 r_work: 0.2848 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9822 Z= 0.154 Angle : 0.502 6.487 13168 Z= 0.252 Chirality : 0.040 0.156 1398 Planarity : 0.004 0.040 1578 Dihedral : 17.293 88.779 1874 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.82 % Allowed : 15.49 % Favored : 82.69 % 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: 1.65 (0.19), residues: 768 sheet: -3.29 (0.87), residues: 20 loop : 1.62 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.016 0.001 PHE A 534 TYR 0.006 0.001 TYR B 22 ARG 0.002 0.000 ARG A 180 *********************** 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 143 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.066 Fit side-chains REVERT: A 9 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: A 284 LYS cc_start: 0.7752 (ttmp) cc_final: 0.7404 (tmtm) REVERT: A 285 GLU cc_start: 0.7995 (mp0) cc_final: 0.7679 (mp0) REVERT: A 370 THR cc_start: 0.8543 (p) cc_final: 0.8228 (t) REVERT: A 459 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: A 463 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7538 (pp30) REVERT: A 511 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: A 545 MET cc_start: 0.8367 (ttp) cc_final: 0.7851 (ttt) REVERT: A 575 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6556 (tpt) REVERT: A 595 GLN cc_start: 0.7479 (tp-100) cc_final: 0.6875 (tp40) REVERT: A 601 GLU cc_start: 0.7988 (mp0) cc_final: 0.7336 (mp0) REVERT: B 9 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: B 284 LYS cc_start: 0.7757 (ttmp) cc_final: 0.7409 (tmtm) REVERT: B 285 GLU cc_start: 0.8017 (mp0) cc_final: 0.7704 (mp0) REVERT: B 370 THR cc_start: 0.8544 (p) cc_final: 0.8224 (t) REVERT: B 459 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: B 463 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7615 (pp30) REVERT: B 511 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: B 545 MET cc_start: 0.8369 (ttp) cc_final: 0.7854 (ttt) REVERT: B 575 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6562 (tpt) REVERT: B 582 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7162 (mm-40) REVERT: B 595 GLN cc_start: 0.7474 (tp-100) cc_final: 0.6868 (tp40) REVERT: B 601 GLU cc_start: 0.7875 (mp0) cc_final: 0.7204 (mp0) outliers start: 17 outliers final: 4 residues processed: 135 average time/residue: 1.5757 time to fit residues: 226.3935 Evaluate side-chains 140 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 582 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 77 optimal weight: 5.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 270 ASN B 13 ASN B 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.135051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102629 restraints weight = 9545.219| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.43 r_work: 0.2848 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9822 Z= 0.152 Angle : 0.500 6.501 13168 Z= 0.251 Chirality : 0.040 0.157 1398 Planarity : 0.004 0.040 1578 Dihedral : 16.933 86.618 1874 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.50 % Allowed : 16.03 % Favored : 82.48 % 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: 2.34 (0.25), residues: 1096 helix: 1.68 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.53 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 247 HIS 0.002 0.001 HIS B 531 PHE 0.015 0.001 PHE A 298 TYR 0.006 0.001 TYR B 22 ARG 0.002 0.000 ARG A 180 ********************** 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 138 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.005 Fit side-chains REVERT: A 9 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: A 284 LYS cc_start: 0.7793 (ttmp) cc_final: 0.7441 (tmtm) REVERT: A 285 GLU cc_start: 0.8002 (mp0) cc_final: 0.7684 (mp0) REVERT: A 370 THR cc_start: 0.8546 (p) cc_final: 0.8229 (t) REVERT: A 463 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.7513 (pp30) REVERT: A 511 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: A 545 MET cc_start: 0.8363 (ttp) cc_final: 0.7842 (ttt) REVERT: A 575 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6525 (tpt) REVERT: A 595 GLN cc_start: 0.7476 (tp-100) cc_final: 0.6880 (tp40) REVERT: A 601 GLU cc_start: 0.8005 (mp0) cc_final: 0.7356 (mp0) REVERT: B 9 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: B 284 LYS cc_start: 0.7744 (ttmp) cc_final: 0.7399 (tmtm) REVERT: B 285 GLU cc_start: 0.7963 (mp0) cc_final: 0.7661 (mp0) REVERT: B 370 THR cc_start: 0.8541 (p) cc_final: 0.8224 (t) REVERT: B 459 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: B 463 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7615 (pp30) REVERT: B 511 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: B 545 MET cc_start: 0.8362 (ttp) cc_final: 0.7843 (ttt) REVERT: B 575 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6542 (tpt) REVERT: B 595 GLN cc_start: 0.7475 (tp-100) cc_final: 0.6882 (tp40) REVERT: B 601 GLU cc_start: 0.7919 (mp0) cc_final: 0.7196 (mp0) outliers start: 14 outliers final: 4 residues processed: 132 average time/residue: 1.5683 time to fit residues: 219.8788 Evaluate side-chains 137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 575 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 270 ASN B 13 ASN B 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.099787 restraints weight = 9501.762| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.41 r_work: 0.2799 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2942 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= 0.220 Angle : 0.563 6.871 13168 Z= 0.282 Chirality : 0.043 0.166 1398 Planarity : 0.005 0.042 1578 Dihedral : 17.355 89.607 1874 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.50 % Allowed : 16.24 % Favored : 82.26 % 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: 1.97 (0.25), residues: 1096 helix: 1.49 (0.19), residues: 766 sheet: -3.19 (0.90), residues: 20 loop : 1.50 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 247 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.002 PHE B 534 TYR 0.008 0.001 TYR B 293 ARG 0.002 0.000 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7409.73 seconds wall clock time: 131 minutes 28.72 seconds (7888.72 seconds total)