Starting phenix.real_space_refine on Thu Jul 2 05:12:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nes_49333/07_2026/9nes_49333.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nes_49333/07_2026/9nes_49333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nes_49333/07_2026/9nes_49333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nes_49333/07_2026/9nes_49333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nes_49333/07_2026/9nes_49333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nes_49333/07_2026/9nes_49333.map" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.084 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 K 2 8.98 5 S 28 5.16 5 C 4584 2.51 5 N 976 2.21 5 O 1061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6651 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1572 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1572 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1572 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1572 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-1': 7, 'POV:plan-2': 6} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-1': 7, 'POV:plan-2': 6} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.26 Number of scatterers: 6651 At special positions: 0 Unit cell: (97.11, 97.11, 63.08, 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) K 2 19.00 S 28 16.00 O 1061 8.00 N 976 7.00 C 4584 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: 0.56 Conformation dependent library (CDL) restraints added in 390.1 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 226 through 248 Processing helix chain 'A' and resid 278 through 298 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.612A pdb=" N ARG A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 3.584A pdb=" N GLN A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 452 through 472 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.670A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 248 Processing helix chain 'B' and resid 278 through 298 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 320 through 326 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.620A pdb=" N ARG B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.586A pdb=" N GLN B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 419 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 452 through 472 Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.668A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 248 Processing helix chain 'C' and resid 278 through 298 Processing helix chain 'C' and resid 311 through 319 Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 369 through 378 removed outlier: 3.621A pdb=" N ARG C 377 " --> pdb=" O LYS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.586A pdb=" N GLN C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 419 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 441 Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 489 removed outlier: 3.669A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 248 Processing helix chain 'D' and resid 278 through 298 Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 369 through 378 removed outlier: 3.611A pdb=" N ARG D 377 " --> pdb=" O LYS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.563A pdb=" N GLN D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 419 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 441 Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 489 removed outlier: 3.674A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1419 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: 0.99 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 920 1.31 - 1.43: 1833 1.43 - 1.55: 3879 1.55 - 1.68: 84 1.68 - 1.80: 44 Bond restraints: 6760 Sorted by residual: bond pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C31 POV D 702 " pdb=" O31 POV D 702 " ideal model delta sigma weight residual 1.327 1.440 -0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C31 POV B 701 " pdb=" O31 POV B 701 " ideal model delta sigma weight residual 1.327 1.440 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.440 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C31 POV A 705 " pdb=" O31 POV A 705 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 6755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 8632 2.05 - 4.09: 272 4.09 - 6.14: 136 6.14 - 8.19: 20 8.19 - 10.23: 12 Bond angle restraints: 9072 Sorted by residual: angle pdb=" C32 POV D 702 " pdb=" C31 POV D 702 " pdb=" O31 POV D 702 " ideal model delta sigma weight residual 110.66 120.89 -10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C32 POV B 701 " pdb=" C31 POV B 701 " pdb=" O31 POV B 701 " ideal model delta sigma weight residual 110.66 120.88 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C32 POV A 701 " pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 110.66 120.86 -10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C32 POV C 702 " pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " ideal model delta sigma weight residual 110.66 120.82 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C32 POV C 706 " pdb=" C31 POV C 706 " pdb=" O31 POV C 706 " ideal model delta sigma weight residual 110.66 120.34 -9.68 3.00e+00 1.11e-01 1.04e+01 ... (remaining 9067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.27: 3573 20.27 - 40.53: 273 40.53 - 60.80: 74 60.80 - 81.07: 4 81.07 - 101.34: 4 Dihedral angle restraints: 3928 sinusoidal: 1612 harmonic: 2316 Sorted by residual: dihedral pdb=" C3 POV B 701 " pdb=" C31 POV B 701 " pdb=" O31 POV B 701 " pdb=" C32 POV B 701 " ideal model delta sinusoidal sigma weight residual 172.61 71.27 101.34 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" C3 POV D 702 " pdb=" C31 POV D 702 " pdb=" O31 POV D 702 " pdb=" C32 POV D 702 " ideal model delta sinusoidal sigma weight residual 172.61 71.47 101.14 1 3.00e+01 1.11e-03 1.27e+01 dihedral pdb=" C3 POV A 701 " pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " pdb=" C32 POV A 701 " ideal model delta sinusoidal sigma weight residual 172.61 71.59 101.02 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 3925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 575 0.032 - 0.063: 331 0.063 - 0.095: 138 0.095 - 0.127: 43 0.127 - 0.158: 5 Chirality restraints: 1092 Sorted by residual: chirality pdb=" CA LEU B 472 " pdb=" N LEU B 472 " pdb=" C LEU B 472 " pdb=" CB LEU B 472 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA LEU D 472 " pdb=" N LEU D 472 " pdb=" C LEU D 472 " pdb=" CB LEU D 472 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA LEU A 472 " pdb=" N LEU A 472 " pdb=" C LEU A 472 " pdb=" CB LEU A 472 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1089 not shown) Planarity restraints: 1052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 472 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO C 473 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 473 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 473 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 472 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO D 473 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 473 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 473 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 472 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 473 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.046 5.00e-02 4.00e+02 ... (remaining 1049 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 2001 2.82 - 3.40: 7259 3.40 - 3.98: 12377 3.98 - 4.56: 18842 4.56 - 5.14: 26587 Nonbonded interactions: 67066 Sorted by model distance: nonbonded pdb=" OD1 ASP D 447 " pdb=" OG1 THR D 449 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP A 447 " pdb=" OG1 THR A 449 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP C 447 " pdb=" OG1 THR C 449 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP B 447 " pdb=" OG1 THR B 449 " model vdw 2.244 3.040 nonbonded pdb=" O HOH A 802 " pdb=" O HOH B 801 " model vdw 2.249 3.040 ... (remaining 67061 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 226 through 489 or (resid 701 and (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 C2 \ 9 or name O21 or name O22)) or (resid 702 and (name C31 or name C32 or name C33 \ or name C34 or name C35)) or (resid 703 and (name C32 or name C33 or name C34 or \ name C35 or name C36)) or (resid 704 and (name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39)) or (resid 705 and (nam \ e C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38)) or (resid 706 and (name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38)) or (resid 707 and (name C33 or name C34 or name C35 or nam \ e C36 or name C37)))) selection = (chain 'B' and (resid 226 through 489 or (resid 701 and (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 C2 \ 9 or name O21 or name O22)) or (resid 702 and (name C31 or name C32 or name C33 \ or name C34 or name C35)) or (resid 703 and (name C32 or name C33 or name C34 or \ name C35 or name C36)) or (resid 704 and (name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39)) or (resid 705 and (nam \ e C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38)) or (resid 706 and (name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38)) or (resid 707 and (name C33 or name C34 or name C35 or nam \ e C36 or name C37)))) selection = (chain 'C' and (resid 226 through 489 or (resid 701 and (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 C2 \ 9 or name O21 or name O22)) or (resid 702 and (name C31 or name C32 or name C33 \ or name C34 or name C35)) or (resid 703 and (name C32 or name C33 or name C34 or \ name C35 or name C36)) or resid 704 or (resid 705 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or (resid \ 706 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) \ or (resid 707 and (name C33 or name C34 or name C35 or name C36 or name C37)))) \ selection = (chain 'D' and (resid 226 through 489 or (resid 701 and (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 C2 \ 9 or name O21 or name O22)) or (resid 702 and (name C31 or name C32 or name C33 \ or name C34 or name C35)) or (resid 703 and (name C32 or name C33 or name C34 or \ name C35 or name C36)) or resid 704 or (resid 705 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) or (resid \ 706 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38)) \ or (resid 707 and (name C33 or name C34 or name C35 or name C36 or name C37)))) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.790 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 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 : 0.011 0.114 6760 Z= 0.494 Angle : 1.035 10.231 9072 Z= 0.450 Chirality : 0.046 0.158 1092 Planarity : 0.009 0.084 1052 Dihedral : 16.435 101.337 2416 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.29), residues: 768 helix: -0.27 (0.19), residues: 628 sheet: None (None), residues: 0 loop : -0.64 (0.62), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 377 TYR 0.009 0.002 TYR A 445 PHE 0.016 0.002 PHE A 324 TRP 0.006 0.001 TRP B 454 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.49 ( 6760) covalent geometry : angle 1.03481 / 0.45 ( 9072) hydrogen bonds : bond 0.10598 / 7.31 ( 497) hydrogen bonds : angle 4.38817 / 2.98 ( 1419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.6286 time to fit residues: 77.5189 Evaluate side-chains 114 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.103225 restraints weight = 7380.367| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.66 r_work: 0.3012 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6760 Z= 0.137 Angle : 0.562 5.578 9072 Z= 0.288 Chirality : 0.042 0.134 1092 Planarity : 0.006 0.044 1052 Dihedral : 11.618 55.834 1076 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.59 % Allowed : 5.00 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.31), residues: 768 helix: 1.22 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.37 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 368 TYR 0.007 0.001 TYR A 323 PHE 0.011 0.001 PHE B 244 TRP 0.005 0.001 TRP D 454 HIS 0.001 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6760) covalent geometry : angle 0.56250 / 0.29 ( 9072) hydrogen bonds : bond 0.04622 / 3.10 ( 497) hydrogen bonds : angle 3.46011 / 2.43 ( 1419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.183 Fit side-chains REVERT: A 317 ILE cc_start: 0.8510 (mm) cc_final: 0.8303 (mt) REVERT: A 395 GLU cc_start: 0.8044 (mp0) cc_final: 0.7833 (mp0) REVERT: B 317 ILE cc_start: 0.8501 (mm) cc_final: 0.8300 (mt) REVERT: B 395 GLU cc_start: 0.8035 (mp0) cc_final: 0.7824 (mp0) REVERT: C 317 ILE cc_start: 0.8526 (mm) cc_final: 0.8324 (mt) REVERT: C 395 GLU cc_start: 0.8033 (mp0) cc_final: 0.7821 (mp0) REVERT: D 317 ILE cc_start: 0.8501 (mm) cc_final: 0.8295 (mt) REVERT: D 395 GLU cc_start: 0.8031 (mp0) cc_final: 0.7819 (mp0) outliers start: 4 outliers final: 0 residues processed: 128 average time/residue: 0.4791 time to fit residues: 64.7100 Evaluate side-chains 121 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100539 restraints weight = 7351.481| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.67 r_work: 0.2972 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6760 Z= 0.182 Angle : 0.579 5.678 9072 Z= 0.299 Chirality : 0.044 0.144 1092 Planarity : 0.006 0.043 1052 Dihedral : 9.809 56.114 1076 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.74 % Allowed : 9.71 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.31), residues: 768 helix: 1.65 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.30 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 377 TYR 0.007 0.002 TYR A 485 PHE 0.011 0.001 PHE C 244 TRP 0.006 0.001 TRP B 454 HIS 0.002 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 6760) covalent geometry : angle 0.57915 / 0.30 ( 9072) hydrogen bonds : bond 0.05224 / 3.52 ( 497) hydrogen bonds : angle 3.52001 / 2.46 ( 1419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.289 Fit side-chains REVERT: A 317 ILE cc_start: 0.8472 (mm) cc_final: 0.8269 (mt) REVERT: D 317 ILE cc_start: 0.8461 (mm) cc_final: 0.8258 (mt) outliers start: 5 outliers final: 1 residues processed: 123 average time/residue: 0.5039 time to fit residues: 65.3785 Evaluate side-chains 118 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.104212 restraints weight = 7411.397| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.69 r_work: 0.3030 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6760 Z= 0.120 Angle : 0.523 5.571 9072 Z= 0.267 Chirality : 0.040 0.134 1092 Planarity : 0.005 0.042 1052 Dihedral : 7.822 50.004 1076 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.18 % Allowed : 10.00 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.31), residues: 768 helix: 2.09 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.34 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 297 TYR 0.007 0.001 TYR D 323 PHE 0.009 0.001 PHE D 244 TRP 0.004 0.001 TRP B 454 HIS 0.001 0.001 HIS D 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6760) covalent geometry : angle 0.52326 / 0.27 ( 9072) hydrogen bonds : bond 0.04253 / 2.85 ( 497) hydrogen bonds : angle 3.26944 / 2.30 ( 1419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.248 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 120 average time/residue: 0.4963 time to fit residues: 62.9586 Evaluate side-chains 109 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104581 restraints weight = 7463.115| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.71 r_work: 0.3030 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6760 Z= 0.120 Angle : 0.521 5.636 9072 Z= 0.265 Chirality : 0.040 0.133 1092 Planarity : 0.005 0.046 1052 Dihedral : 7.165 43.558 1076 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.03 % Allowed : 12.21 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.32), residues: 768 helix: 2.32 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.22 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 377 TYR 0.006 0.001 TYR D 323 PHE 0.010 0.001 PHE D 244 TRP 0.004 0.001 TRP B 454 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 6760) covalent geometry : angle 0.52060 / 0.27 ( 9072) hydrogen bonds : bond 0.04195 / 2.81 ( 497) hydrogen bonds : angle 3.19988 / 2.25 ( 1419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.257 Fit side-chains REVERT: A 324 PHE cc_start: 0.8035 (m-80) cc_final: 0.7615 (m-80) REVERT: B 324 PHE cc_start: 0.8023 (m-80) cc_final: 0.7603 (m-80) REVERT: C 324 PHE cc_start: 0.8022 (m-80) cc_final: 0.7602 (m-80) REVERT: D 324 PHE cc_start: 0.8003 (m-80) cc_final: 0.7589 (m-80) outliers start: 7 outliers final: 0 residues processed: 115 average time/residue: 0.4717 time to fit residues: 57.4204 Evaluate side-chains 105 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 63 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102401 restraints weight = 7463.980| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.71 r_work: 0.2998 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6760 Z= 0.139 Angle : 0.543 5.727 9072 Z= 0.279 Chirality : 0.041 0.137 1092 Planarity : 0.005 0.049 1052 Dihedral : 7.183 37.562 1076 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.32 % Allowed : 12.79 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.32), residues: 768 helix: 2.37 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.24 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 377 TYR 0.006 0.001 TYR A 485 PHE 0.011 0.001 PHE C 244 TRP 0.005 0.001 TRP B 454 HIS 0.001 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6760) covalent geometry : angle 0.54282 / 0.28 ( 9072) hydrogen bonds : bond 0.04535 / 3.04 ( 497) hydrogen bonds : angle 3.25216 / 2.28 ( 1419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.214 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 112 average time/residue: 0.5156 time to fit residues: 60.7680 Evaluate side-chains 112 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.102148 restraints weight = 7360.762| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.69 r_work: 0.2995 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6760 Z= 0.145 Angle : 0.557 5.761 9072 Z= 0.286 Chirality : 0.042 0.138 1092 Planarity : 0.005 0.052 1052 Dihedral : 7.143 33.890 1076 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.32 % Allowed : 13.09 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.32), residues: 768 helix: 2.40 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.24 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 377 TYR 0.006 0.001 TYR A 485 PHE 0.011 0.001 PHE C 244 TRP 0.005 0.001 TRP B 454 HIS 0.001 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 6760) covalent geometry : angle 0.55698 / 0.29 ( 9072) hydrogen bonds : bond 0.04620 / 3.10 ( 497) hydrogen bonds : angle 3.26973 / 2.29 ( 1419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.151 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 109 average time/residue: 0.4358 time to fit residues: 50.1937 Evaluate side-chains 109 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102302 restraints weight = 7410.311| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.69 r_work: 0.3004 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6760 Z= 0.137 Angle : 0.553 5.748 9072 Z= 0.284 Chirality : 0.041 0.136 1092 Planarity : 0.005 0.052 1052 Dihedral : 6.923 32.372 1076 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.76 % Allowed : 13.97 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.32), residues: 768 helix: 2.44 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.21 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 377 TYR 0.006 0.001 TYR D 485 PHE 0.010 0.001 PHE D 244 TRP 0.005 0.001 TRP B 454 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6760) covalent geometry : angle 0.55263 / 0.28 ( 9072) hydrogen bonds : bond 0.04460 / 2.99 ( 497) hydrogen bonds : angle 3.22947 / 2.27 ( 1419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.154 Fit side-chains outliers start: 12 outliers final: 1 residues processed: 112 average time/residue: 0.3730 time to fit residues: 44.1184 Evaluate side-chains 109 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 chunk 71 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.104144 restraints weight = 7346.216| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.69 r_work: 0.3028 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6760 Z= 0.126 Angle : 0.543 5.777 9072 Z= 0.278 Chirality : 0.040 0.133 1092 Planarity : 0.005 0.053 1052 Dihedral : 6.524 30.261 1076 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.29 % Allowed : 15.88 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.32), residues: 768 helix: 2.54 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.12 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 377 TYR 0.006 0.001 TYR B 323 PHE 0.009 0.001 PHE C 244 TRP 0.004 0.001 TRP B 454 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 6760) covalent geometry : angle 0.54310 / 0.28 ( 9072) hydrogen bonds : bond 0.04162 / 2.78 ( 497) hydrogen bonds : angle 3.14928 / 2.21 ( 1419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.162 Fit side-chains REVERT: A 324 PHE cc_start: 0.7998 (m-80) cc_final: 0.7588 (m-80) REVERT: A 403 LEU cc_start: 0.8452 (tp) cc_final: 0.8127 (mt) REVERT: B 324 PHE cc_start: 0.7996 (m-80) cc_final: 0.7588 (m-80) REVERT: B 403 LEU cc_start: 0.8441 (tp) cc_final: 0.8116 (mt) REVERT: C 324 PHE cc_start: 0.7996 (m-80) cc_final: 0.7588 (m-80) REVERT: C 403 LEU cc_start: 0.8441 (tp) cc_final: 0.8113 (mt) REVERT: D 324 PHE cc_start: 0.8016 (m-80) cc_final: 0.7567 (m-80) REVERT: D 403 LEU cc_start: 0.8441 (tp) cc_final: 0.8118 (mt) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.4426 time to fit residues: 49.0241 Evaluate side-chains 105 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 75 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102568 restraints weight = 7423.665| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.70 r_work: 0.3007 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6760 Z= 0.139 Angle : 0.562 5.754 9072 Z= 0.289 Chirality : 0.041 0.136 1092 Planarity : 0.005 0.054 1052 Dihedral : 6.747 34.245 1076 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.88 % Allowed : 15.88 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.31), residues: 768 helix: 2.49 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.16 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 377 TYR 0.006 0.001 TYR B 485 PHE 0.011 0.001 PHE A 244 TRP 0.005 0.001 TRP B 454 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6760) covalent geometry : angle 0.56205 / 0.29 ( 9072) hydrogen bonds : bond 0.04451 / 2.99 ( 497) hydrogen bonds : angle 3.19851 / 2.24 ( 1419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.156 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 110 average time/residue: 0.4297 time to fit residues: 49.9599 Evaluate side-chains 109 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 0.0370 chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104794 restraints weight = 7292.246| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.69 r_work: 0.3036 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6760 Z= 0.123 Angle : 0.541 5.811 9072 Z= 0.277 Chirality : 0.040 0.130 1092 Planarity : 0.005 0.053 1052 Dihedral : 6.371 28.688 1076 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.15 % Allowed : 16.62 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.32), residues: 768 helix: 2.57 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -0.11 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 377 TYR 0.006 0.001 TYR B 323 PHE 0.008 0.001 PHE B 244 TRP 0.004 0.001 TRP B 454 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6760) covalent geometry : angle 0.54125 / 0.28 ( 9072) hydrogen bonds : bond 0.04083 / 2.73 ( 497) hydrogen bonds : angle 3.10950 / 2.19 ( 1419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.66 seconds wall clock time: 37 minutes 46.69 seconds (2266.69 seconds total)