Starting phenix.real_space_refine on Sun Dec 29 04:24:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tei_41187/12_2024/8tei_41187.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tei_41187/12_2024/8tei_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_41187/12_2024/8tei_41187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tei_41187/12_2024/8tei_41187.map" model { file = "/net/cci-nas-00/data/ceres_data/8tei_41187/12_2024/8tei_41187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tei_41187/12_2024/8tei_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-5532/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: 6.21, per 1000 atoms: 0.63 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: 2.79 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: 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: 1.03 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: 2.99 Time building geometry restraints manager: 3.07 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: 0.00 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 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: 1.720 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.470 Find NCS groups from input model: 0.350 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- 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 : 1.051 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: 1.3353 time to fit residues: 164.4121 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 : 1.077 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 1.064 Fit side-chains REVERT: A 80 MET cc_start: 0.8951 (mtp) cc_final: 0.8724 (mtm) REVERT: A 459 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: A 575 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.6930 (tpt) REVERT: A 595 GLN cc_start: 0.7277 (tp-100) cc_final: 0.6855 (tp40) REVERT: A 603 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: B 459 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: B 595 GLN cc_start: 0.7259 (tp-100) cc_final: 0.6798 (tp40) REVERT: B 603 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7437 (mp0) outliers start: 21 outliers final: 7 residues processed: 137 average time/residue: 1.6333 time to fit residues: 236.6395 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 : 1.026 ------------------------------------------------------------------------------- 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 55 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 320 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1720 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= 0.147 Angle : 0.495 6.461 13168 Z= 0.248 Chirality : 0.041 0.154 1398 Planarity : 0.004 0.038 1578 Dihedral : 19.902 123.308 1874 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.56 % Allowed : 13.14 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.26), residues: 1096 helix: 1.71 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 1.37 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.002 0.001 HIS B 364 PHE 0.013 0.001 PHE A 534 TYR 0.008 0.001 TYR A 22 ARG 0.005 0.000 ARG A 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 147 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.002 Fit side-chains REVERT: A 370 THR cc_start: 0.8497 (p) cc_final: 0.8028 (t) REVERT: A 462 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: A 463 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7416 (pp30) REVERT: A 575 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6931 (tpt) REVERT: A 595 GLN cc_start: 0.7220 (tp-100) cc_final: 0.6770 (tp40) REVERT: A 603 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: B 463 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7367 (pp30) REVERT: B 575 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6931 (tpt) REVERT: B 595 GLN cc_start: 0.7222 (tp-100) cc_final: 0.6772 (tp40) outliers start: 24 outliers final: 2 residues processed: 139 average time/residue: 1.5155 time to fit residues: 224.0364 Evaluate side-chains 121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 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 603 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9822 Z= 0.256 Angle : 0.605 7.100 13168 Z= 0.303 Chirality : 0.045 0.181 1398 Planarity : 0.005 0.044 1578 Dihedral : 20.142 107.146 1874 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.78 % Allowed : 13.46 % 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: 1.82 (0.25), residues: 1096 helix: 1.33 (0.19), residues: 770 sheet: -2.18 (0.84), residues: 20 loop : 1.50 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 247 HIS 0.003 0.001 HIS B 364 PHE 0.017 0.002 PHE B 298 TYR 0.014 0.002 TYR B 293 ARG 0.003 0.001 ARG B 581 *********************** 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 149 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.062 Fit side-chains REVERT: A 24 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: A 370 THR cc_start: 0.8608 (p) cc_final: 0.8162 (t) REVERT: A 463 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8237 (pp30) REVERT: A 582 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: A 595 GLN cc_start: 0.7393 (tp-100) cc_final: 0.6918 (tp40) REVERT: A 603 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: B 24 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: B 370 THR cc_start: 0.8609 (p) cc_final: 0.8155 (t) REVERT: B 459 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: B 463 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8230 (pp30) REVERT: B 582 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: B 595 GLN cc_start: 0.7392 (tp-100) cc_final: 0.6904 (tp40) REVERT: B 603 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7424 (mp0) outliers start: 26 outliers final: 6 residues processed: 138 average time/residue: 1.6233 time to fit residues: 237.0807 Evaluate side-chains 137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 281 THR 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 24 GLN Chi-restraints excluded: chain B residue 281 THR 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 Chi-restraints excluded: chain B residue 603 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- 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 170 GLN B 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2426 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= 0.155 Angle : 0.509 7.103 13168 Z= 0.256 Chirality : 0.041 0.160 1398 Planarity : 0.004 0.040 1578 Dihedral : 19.037 90.064 1874 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.35 % Allowed : 13.89 % 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: 2.12 (0.25), residues: 1096 helix: 1.59 (0.19), residues: 766 sheet: -2.65 (0.84), residues: 20 loop : 1.54 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.014 0.001 PHE B 534 TYR 0.008 0.001 TYR B 293 ARG 0.002 0.000 ARG B 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 147 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.097 Fit side-chains REVERT: A 370 THR cc_start: 0.8597 (p) cc_final: 0.8178 (t) REVERT: A 459 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: A 462 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7196 (pt0) REVERT: A 463 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7809 (pp30) REVERT: A 575 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6924 (tpt) REVERT: A 582 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7214 (mm-40) REVERT: A 595 GLN cc_start: 0.7293 (tp-100) cc_final: 0.6866 (tp40) REVERT: B 370 THR cc_start: 0.8607 (p) cc_final: 0.8180 (t) REVERT: B 462 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7190 (pt0) REVERT: B 463 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7788 (pp30) REVERT: B 575 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6925 (tpt) REVERT: B 582 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7204 (mm-40) REVERT: B 595 GLN cc_start: 0.7294 (tp-100) cc_final: 0.6860 (tp40) REVERT: B 601 GLU cc_start: 0.7845 (mp0) cc_final: 0.6880 (mp0) REVERT: B 603 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7272 (mp0) outliers start: 22 outliers final: 2 residues processed: 141 average time/residue: 1.6253 time to fit residues: 243.2274 Evaluate side-chains 136 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 462 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 B residue 462 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 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 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.0020 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2465 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 : 0.503 6.640 13168 Z= 0.251 Chirality : 0.040 0.155 1398 Planarity : 0.004 0.039 1578 Dihedral : 17.934 88.473 1874 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.03 % Allowed : 14.32 % Favored : 83.65 % 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: 2.22 (0.26), residues: 1096 helix: 1.63 (0.19), residues: 772 sheet: -2.85 (0.87), residues: 20 loop : 1.71 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.014 0.001 PHE B 298 TYR 0.008 0.001 TYR B 293 ARG 0.002 0.000 ARG B 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: 19 poor density : 128 time to evaluate : 1.345 Fit side-chains REVERT: A 370 THR cc_start: 0.8619 (p) cc_final: 0.8221 (t) REVERT: A 459 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: A 462 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: A 463 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7768 (pp30) REVERT: A 575 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6923 (tpt) REVERT: A 595 GLN cc_start: 0.7288 (tp-100) cc_final: 0.6835 (tp40) REVERT: A 601 GLU cc_start: 0.7795 (mp0) cc_final: 0.7253 (mp0) REVERT: B 370 THR cc_start: 0.8631 (p) cc_final: 0.8220 (t) REVERT: B 459 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: B 462 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: B 463 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7774 (pp30) REVERT: B 575 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.6903 (tpt) REVERT: B 595 GLN cc_start: 0.7293 (tp-100) cc_final: 0.6821 (tp40) REVERT: B 601 GLU cc_start: 0.7813 (mp0) cc_final: 0.6850 (mp0) REVERT: B 603 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7247 (mp0) outliers start: 19 outliers final: 4 residues processed: 139 average time/residue: 1.6156 time to fit residues: 238.4251 Evaluate side-chains 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 462 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 B residue 281 THR Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 462 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 603 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2597 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= 0.165 Angle : 0.514 6.764 13168 Z= 0.258 Chirality : 0.041 0.159 1398 Planarity : 0.004 0.039 1578 Dihedral : 17.445 88.895 1874 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.82 % Allowed : 14.74 % Favored : 83.44 % 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: 1.62 (0.19), residues: 770 sheet: -3.04 (0.85), residues: 20 loop : 1.74 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.002 0.001 HIS B 364 PHE 0.014 0.001 PHE B 534 TYR 0.009 0.001 TYR B 293 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 138 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.029 Fit side-chains REVERT: A 370 THR cc_start: 0.8628 (p) cc_final: 0.8243 (t) REVERT: A 459 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: A 462 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: A 463 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7862 (pp30) REVERT: A 511 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: A 575 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6874 (tpt) REVERT: A 595 GLN cc_start: 0.7325 (tp-100) cc_final: 0.6879 (tp40) REVERT: A 601 GLU cc_start: 0.7890 (mp0) cc_final: 0.7309 (mp0) REVERT: B 370 THR cc_start: 0.8656 (p) cc_final: 0.8266 (t) REVERT: B 459 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: B 462 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: B 463 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.7918 (pp30) REVERT: B 511 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: B 575 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6874 (tpt) REVERT: B 595 GLN cc_start: 0.7329 (tp-100) cc_final: 0.6881 (tp40) REVERT: B 601 GLU cc_start: 0.7843 (mp0) cc_final: 0.6846 (mp0) REVERT: B 603 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7248 (mp0) outliers start: 17 outliers final: 2 residues processed: 131 average time/residue: 1.6447 time to fit residues: 227.9521 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 : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 462 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 459 GLU Chi-restraints excluded: chain B residue 462 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 603 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 270 ASN B 13 ASN B 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9822 Z= 0.231 Angle : 0.564 7.015 13168 Z= 0.283 Chirality : 0.043 0.165 1398 Planarity : 0.005 0.042 1578 Dihedral : 17.836 92.369 1874 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.92 % Allowed : 14.53 % Favored : 83.55 % 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: 1.47 (0.19), residues: 768 sheet: -2.99 (0.87), residues: 20 loop : 1.60 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 247 HIS 0.003 0.001 HIS B 364 PHE 0.016 0.002 PHE B 298 TYR 0.008 0.001 TYR B 495 ARG 0.002 0.000 ARG B 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 141 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.076 Fit side-chains REVERT: A 284 LYS cc_start: 0.7880 (ttmp) cc_final: 0.7601 (tttp) REVERT: A 370 THR cc_start: 0.8589 (p) cc_final: 0.8195 (t) REVERT: A 459 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: A 463 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: A 511 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: A 595 GLN cc_start: 0.7381 (tp-100) cc_final: 0.6928 (tp40) REVERT: A 601 GLU cc_start: 0.7871 (mp0) cc_final: 0.7292 (mp0) REVERT: B 284 LYS cc_start: 0.7883 (ttmp) cc_final: 0.7602 (tttp) REVERT: B 370 THR cc_start: 0.8583 (p) cc_final: 0.8187 (t) REVERT: B 459 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: B 463 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8130 (pp30) REVERT: B 511 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: B 595 GLN cc_start: 0.7380 (tp-100) cc_final: 0.6925 (tp40) REVERT: B 603 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7315 (mp0) outliers start: 18 outliers final: 7 residues processed: 134 average time/residue: 1.6135 time to fit residues: 229.0470 Evaluate side-chains 135 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 511 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 372 LYS 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 603 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9822 Z= 0.196 Angle : 0.541 7.078 13168 Z= 0.273 Chirality : 0.042 0.165 1398 Planarity : 0.004 0.041 1578 Dihedral : 17.695 93.320 1874 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.82 % Allowed : 15.06 % Favored : 83.12 % 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: 2.03 (0.25), residues: 1096 helix: 1.51 (0.19), residues: 766 sheet: -3.14 (0.86), residues: 20 loop : 1.60 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.002 0.001 HIS B 364 PHE 0.016 0.001 PHE B 534 TYR 0.007 0.001 TYR B 293 ARG 0.002 0.000 ARG B 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 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.920 Fit side-chains REVERT: A 370 THR cc_start: 0.8591 (p) cc_final: 0.8209 (t) REVERT: A 459 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: A 463 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7956 (pp30) REVERT: A 511 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: A 575 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6884 (tpt) REVERT: A 595 GLN cc_start: 0.7351 (tp-100) cc_final: 0.6914 (tp40) REVERT: B 284 LYS cc_start: 0.7917 (ttmp) cc_final: 0.7627 (tttp) REVERT: B 370 THR cc_start: 0.8597 (p) cc_final: 0.8203 (t) REVERT: B 459 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: B 463 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7979 (pp30) REVERT: B 511 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: B 575 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6886 (tpt) REVERT: B 595 GLN cc_start: 0.7352 (tp-100) cc_final: 0.6907 (tp40) outliers start: 17 outliers final: 4 residues processed: 127 average time/residue: 1.5204 time to fit residues: 205.3626 Evaluate side-chains 131 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LYS 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 281 THR 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 49 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 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 13 ASN A 270 ASN B 13 ASN B 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2813 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= 0.161 Angle : 0.513 6.798 13168 Z= 0.258 Chirality : 0.041 0.158 1398 Planarity : 0.004 0.040 1578 Dihedral : 17.246 91.663 1874 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.50 % Allowed : 15.38 % Favored : 83.12 % 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: 2.29 (0.25), residues: 1096 helix: 1.63 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.56 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.016 0.001 PHE B 534 TYR 0.006 0.001 TYR B 293 ARG 0.002 0.000 ARG B 113 ********************** 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 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.094 Fit side-chains REVERT: A 284 LYS cc_start: 0.7872 (ttmp) cc_final: 0.7580 (tttm) REVERT: A 370 THR cc_start: 0.8631 (p) cc_final: 0.8256 (t) REVERT: A 459 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: A 463 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7861 (pp30) REVERT: A 511 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: A 575 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.6873 (tpt) REVERT: A 595 GLN cc_start: 0.7319 (tp-100) cc_final: 0.6889 (tp40) REVERT: A 601 GLU cc_start: 0.7877 (mp0) cc_final: 0.7347 (mp0) REVERT: B 284 LYS cc_start: 0.7881 (ttmp) cc_final: 0.7605 (tttm) REVERT: B 370 THR cc_start: 0.8656 (p) cc_final: 0.8276 (t) REVERT: B 459 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: B 463 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7788 (pp30) REVERT: B 511 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: B 575 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6871 (tpt) REVERT: B 595 GLN cc_start: 0.7323 (tp-100) cc_final: 0.6880 (tp40) REVERT: B 601 GLU cc_start: 0.7823 (mp0) cc_final: 0.7202 (mp0) outliers start: 14 outliers final: 6 residues processed: 127 average time/residue: 1.4973 time to fit residues: 202.0098 Evaluate side-chains 137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 372 LYS 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 281 THR Chi-restraints excluded: chain B residue 372 LYS 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 80 optimal weight: 0.0870 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.135581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103437 restraints weight = 9511.030| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.43 r_work: 0.2873 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2857 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= 0.142 Angle : 0.494 6.533 13168 Z= 0.248 Chirality : 0.040 0.152 1398 Planarity : 0.004 0.039 1578 Dihedral : 16.631 89.948 1874 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.39 % Allowed : 15.81 % 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: 2.50 (0.25), residues: 1096 helix: 1.86 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 1.44 (0.35), residues: 342 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 0.014 0.001 PHE B 534 TYR 0.006 0.001 TYR A 22 ARG 0.002 0.000 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3832.41 seconds wall clock time: 69 minutes 35.79 seconds (4175.79 seconds total)