Starting phenix.real_space_refine on Thu Jul 2 19:25:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8blp_16112/07_2026/8blp_16112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blp_16112/07_2026/8blp_16112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8blp_16112/07_2026/8blp_16112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blp_16112/07_2026/8blp_16112.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8blp_16112/07_2026/8blp_16112.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8blp_16112/07_2026/8blp_16112.cif" model { file = "/net/cci-nas-00/data/ceres_data/8blp_16112/07_2026/8blp_16112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blp_16112/07_2026/8blp_16112.cif" } resolution = 2.6 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= 0.004 sd= 0.119 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 6 5.49 5 S 87 5.16 5 C 6351 2.51 5 N 1287 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 9378 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2699 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 334} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2699 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 334} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2699 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 334} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 405 Unusual residues: {'5D3': 2, 'LMT': 17, 'PTY': 2, 'Y01': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 150 Chain: "B" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 405 Unusual residues: {'5D3': 2, 'LMT': 17, 'PTY': 2, 'Y01': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 150 Chain: "C" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 405 Unusual residues: {'5D3': 2, 'LMT': 17, 'PTY': 2, 'Y01': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 150 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" CAA 5D3 A 420 " occ=0.40 ... (28 atoms not shown) pdb=" SBD 5D3 A 420 " occ=0.40 residue: pdb=" CAA 5D3 B 422 " occ=0.40 ... (28 atoms not shown) pdb=" SBD 5D3 B 422 " occ=0.40 residue: pdb=" CAA 5D3 C 422 " occ=0.40 ... (28 atoms not shown) pdb=" SBD 5D3 C 422 " occ=0.40 Time building chain proxies: 1.91, per 1000 atoms: 0.20 Number of scatterers: 9378 At special positions: 0 Unit cell: (103.32, 97.58, 72.98, 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 87 16.00 P 6 15.00 O 1647 8.00 N 1287 7.00 C 6351 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: 0.97 Conformation dependent library (CDL) restraints added in 304.4 milliseconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 79.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 42 through 52 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 113 through 119 Processing helix chain 'A' and resid 123 through 136 removed outlier: 3.713A pdb=" N ALA A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 171 Proline residue: A 158 - end of helix removed outlier: 4.267A pdb=" N TRP A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.540A pdb=" N LEU A 217 " --> pdb=" O TRP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.023A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.628A pdb=" N VAL A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 253 Processing helix chain 'A' and resid 253 through 274 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.516A pdb=" N ILE A 281 " --> pdb=" O PRO A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 305 through 331 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.643A pdb=" N VAL A 367 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 385 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 42 through 52 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 74 through 89 Processing helix chain 'B' and resid 89 through 110 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.714A pdb=" N ALA B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 171 Proline residue: B 158 - end of helix removed outlier: 4.267A pdb=" N TRP B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.540A pdb=" N LEU B 217 " --> pdb=" O TRP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.022A pdb=" N ILE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 3.628A pdb=" N VAL B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 253 Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.516A pdb=" N ILE B 281 " --> pdb=" O PRO B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'B' and resid 305 through 331 Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.643A pdb=" N VAL B 367 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 74 through 89 Processing helix chain 'C' and resid 89 through 110 Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 123 through 136 removed outlier: 3.714A pdb=" N ALA C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 171 Proline residue: C 158 - end of helix removed outlier: 4.267A pdb=" N TRP C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.540A pdb=" N LEU C 217 " --> pdb=" O TRP C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 233 removed outlier: 4.022A pdb=" N ILE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 3.629A pdb=" N VAL C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 Processing helix chain 'C' and resid 253 through 274 Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.516A pdb=" N ILE C 281 " --> pdb=" O PRO C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'C' and resid 305 through 331 Processing helix chain 'C' and resid 339 through 352 Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.644A pdb=" N VAL C 367 " --> pdb=" O LEU C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 385 571 hydrogen bonds defined for protein. 1695 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: 1.45 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1245 1.29 - 1.42: 2433 1.42 - 1.55: 5681 1.55 - 1.68: 22 1.68 - 1.81: 150 Bond restraints: 9531 Sorted by residual: bond pdb=" C1' LMT B 404 " pdb=" O5' LMT B 404 " ideal model delta sigma weight residual 1.408 1.488 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1' LMT A 402 " pdb=" O5' LMT A 402 " ideal model delta sigma weight residual 1.408 1.487 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1' LMT C 404 " pdb=" O5' LMT C 404 " ideal model delta sigma weight residual 1.408 1.487 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C30 PTY C 403 " pdb=" O4 PTY C 403 " ideal model delta sigma weight residual 1.331 1.408 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C30 PTY B 403 " pdb=" O4 PTY B 403 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 9526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 12245 3.30 - 6.60: 442 6.60 - 9.90: 100 9.90 - 13.20: 5 13.20 - 16.51: 3 Bond angle restraints: 12795 Sorted by residual: angle pdb=" C CYS A 338 " pdb=" CA CYS A 338 " pdb=" CB CYS A 338 " ideal model delta sigma weight residual 116.63 110.06 6.57 1.16e+00 7.43e-01 3.21e+01 angle pdb=" C CYS C 338 " pdb=" CA CYS C 338 " pdb=" CB CYS C 338 " ideal model delta sigma weight residual 116.63 110.07 6.56 1.16e+00 7.43e-01 3.20e+01 angle pdb=" C CYS B 338 " pdb=" CA CYS B 338 " pdb=" CB CYS B 338 " ideal model delta sigma weight residual 116.63 110.08 6.55 1.16e+00 7.43e-01 3.19e+01 angle pdb=" O11 PTY A 401 " pdb=" P1 PTY A 401 " pdb=" O14 PTY A 401 " ideal model delta sigma weight residual 92.90 109.41 -16.51 3.00e+00 1.11e-01 3.03e+01 angle pdb=" O11 PTY B 403 " pdb=" P1 PTY B 403 " pdb=" O14 PTY B 403 " ideal model delta sigma weight residual 92.90 109.38 -16.48 3.00e+00 1.11e-01 3.02e+01 ... (remaining 12790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 5164 34.69 - 69.39: 329 69.39 - 104.08: 9 104.08 - 138.77: 3 138.77 - 173.47: 3 Dihedral angle restraints: 5508 sinusoidal: 2454 harmonic: 3054 Sorted by residual: dihedral pdb=" CBA 5D3 B 422 " pdb=" CAY 5D3 B 422 " pdb=" CAZ 5D3 B 422 " pdb=" NAX 5D3 B 422 " ideal model delta sinusoidal sigma weight residual 111.34 -75.19 -173.47 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CBA 5D3 C 422 " pdb=" CAY 5D3 C 422 " pdb=" CAZ 5D3 C 422 " pdb=" NAX 5D3 C 422 " ideal model delta sinusoidal sigma weight residual 111.34 -75.21 -173.45 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CBA 5D3 A 420 " pdb=" CAY 5D3 A 420 " pdb=" CAZ 5D3 A 420 " pdb=" NAX 5D3 A 420 " ideal model delta sinusoidal sigma weight residual 111.34 -75.23 -173.43 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 721 0.033 - 0.065: 466 0.065 - 0.098: 156 0.098 - 0.130: 75 0.130 - 0.163: 10 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA PRO A 370 " pdb=" N PRO A 370 " pdb=" C PRO A 370 " pdb=" CB PRO A 370 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CA PRO C 370 " pdb=" N PRO C 370 " pdb=" C PRO C 370 " pdb=" CB PRO C 370 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA PRO B 370 " pdb=" N PRO B 370 " pdb=" C PRO B 370 " pdb=" CB PRO B 370 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 1425 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAY 5D3 B 421 " 0.111 2.00e-02 2.50e+03 9.52e-02 1.36e+02 pdb=" CAZ 5D3 B 421 " -0.037 2.00e-02 2.50e+03 pdb=" CBA 5D3 B 421 " -0.131 2.00e-02 2.50e+03 pdb=" CBB 5D3 B 421 " 0.070 2.00e-02 2.50e+03 pdb=" CBC 5D3 B 421 " 0.090 2.00e-02 2.50e+03 pdb=" SBD 5D3 B 421 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAY 5D3 A 419 " 0.111 2.00e-02 2.50e+03 9.51e-02 1.36e+02 pdb=" CAZ 5D3 A 419 " -0.037 2.00e-02 2.50e+03 pdb=" CBA 5D3 A 419 " -0.130 2.00e-02 2.50e+03 pdb=" CBB 5D3 A 419 " 0.070 2.00e-02 2.50e+03 pdb=" CBC 5D3 A 419 " 0.090 2.00e-02 2.50e+03 pdb=" SBD 5D3 A 419 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAY 5D3 C 421 " -0.110 2.00e-02 2.50e+03 9.51e-02 1.36e+02 pdb=" CAZ 5D3 C 421 " 0.037 2.00e-02 2.50e+03 pdb=" CBA 5D3 C 421 " 0.131 2.00e-02 2.50e+03 pdb=" CBB 5D3 C 421 " -0.070 2.00e-02 2.50e+03 pdb=" CBC 5D3 C 421 " -0.090 2.00e-02 2.50e+03 pdb=" SBD 5D3 C 421 " 0.103 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1343 2.75 - 3.28: 8789 3.28 - 3.82: 16704 3.82 - 4.36: 22613 4.36 - 4.90: 36200 Nonbonded interactions: 85649 Sorted by model distance: nonbonded pdb=" O LYS B 366 " pdb=" O HOH B 501 " model vdw 2.208 3.040 nonbonded pdb=" O LYS A 366 " pdb=" O HOH A 501 " model vdw 2.208 3.040 nonbonded pdb=" O LYS C 366 " pdb=" O HOH C 501 " model vdw 2.208 3.040 nonbonded pdb=" O CYS A 157 " pdb=" OG SER A 161 " model vdw 2.272 3.040 nonbonded pdb=" O CYS C 157 " pdb=" OG SER C 161 " model vdw 2.272 3.040 ... (remaining 85644 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 385 or (resid 402 and (name C1 or name C10 or n \ ame C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ C9 or name O1')) or resid 404 through 406 or (resid 408 and (name C1 or name C2 \ or name C3 or name C4 or name C5 or name C6 or name C7 or name O1')) or resid 4 \ 10 through 412 or (resid 413 through 414 and (name C1 or name C2 or name C3 or n \ ame C4 or name C5 or name C6 or name C7 or name O1')) or (resid 415 and (name C1 \ or name C10 or name C11 or name C2 or name C3 or name C4 or name C5 or name C6 \ or name C7 or name C8 or name C9 or name O1')) or (resid 416 and (name C1 or nam \ e C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O1')) or res \ id 417 through 418)) selection = (chain 'B' and (resid 31 through 385 or resid 402 or (resid 404 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O1')) or \ (resid 405 and (name C1 or name C10 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name O1')) or resid 406 or resid \ 408 or (resid 410 and (name C1 or name C10 or name C2 or name C3 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O1')) or (resid 411 t \ hrough 414 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name O1')) or resid 415 through 417 or (resid 418 and (name C1 or n \ ame C2 or name C3 or name C4 or name C5 or name C6 or name O1')))) selection = (chain 'C' and (resid 31 through 385 or resid 402 or (resid 404 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name O1')) or \ (resid 405 and (name C1 or name C10 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name O1')) or resid 406 or resid \ 408 or (resid 410 and (name C1 or name C10 or name C2 or name C3 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O1')) or (resid 411 t \ hrough 414 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name O1')) or resid 415 through 417 or (resid 418 and (name C1 or n \ ame C2 or name C3 or name C4 or name C5 or name C6 or name O1')))) } 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=0.40 max=1.00 mean=0.99 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: 1.820 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.530 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 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 : 0.010 0.080 9531 Z= 0.436 Angle : 1.371 16.505 12795 Z= 0.543 Chirality : 0.049 0.163 1428 Planarity : 0.008 0.095 1425 Dihedral : 19.660 173.468 3552 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.35 % Allowed : 8.30 % Favored : 91.35 % 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: -1.57 (0.23), residues: 1059 helix: -1.06 (0.16), residues: 780 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 114 TYR 0.014 0.002 TYR B 234 PHE 0.017 0.002 PHE C 288 TRP 0.011 0.002 TRP C 306 HIS 0.005 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00977 / 0.44 ( 9531) covalent geometry : angle 1.37150 / 0.54 (12795) hydrogen bonds : bond 0.13767 / 8.85 ( 571) hydrogen bonds : angle 6.65787 / 4.77 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.334 Fit side-chains REVERT: A 115 SER cc_start: 0.8429 (m) cc_final: 0.8069 (p) REVERT: B 60 ASP cc_start: 0.7941 (t70) cc_final: 0.7659 (t70) outliers start: 3 outliers final: 2 residues processed: 108 average time/residue: 0.4691 time to fit residues: 55.2039 Evaluate side-chains 103 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN B 165 ASN C 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.093089 restraints weight = 10036.060| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.09 r_work: 0.2906 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9531 Z= 0.135 Angle : 0.568 8.033 12795 Z= 0.271 Chirality : 0.040 0.155 1428 Planarity : 0.005 0.046 1425 Dihedral : 20.374 177.224 1814 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.42 % Allowed : 6.81 % Favored : 90.77 % 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: 0.77 (0.25), residues: 1059 helix: 0.62 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 0.61 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.012 0.001 TYR B 369 PHE 0.014 0.001 PHE A 71 TRP 0.011 0.001 TRP C 306 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9531) covalent geometry : angle 0.56841 / 0.27 (12795) hydrogen bonds : bond 0.04688 / 3.09 ( 571) hydrogen bonds : angle 4.49849 / 3.20 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.385 Fit side-chains REVERT: A 115 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7575 (p) REVERT: A 220 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 115 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7680 (p) REVERT: B 206 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8135 (mm) REVERT: C 115 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7577 (p) REVERT: C 212 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7357 (mp) outliers start: 21 outliers final: 7 residues processed: 117 average time/residue: 0.3984 time to fit residues: 51.1680 Evaluate side-chains 116 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN C 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.091741 restraints weight = 9958.963| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.10 r_work: 0.2874 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9531 Z= 0.159 Angle : 0.570 8.760 12795 Z= 0.274 Chirality : 0.041 0.161 1428 Planarity : 0.005 0.045 1425 Dihedral : 18.218 179.458 1812 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.42 % Allowed : 7.61 % Favored : 89.97 % 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: 1.54 (0.25), residues: 1059 helix: 1.19 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 0.85 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.013 0.001 TYR C 369 PHE 0.014 0.002 PHE A 288 TRP 0.010 0.001 TRP B 306 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9531) covalent geometry : angle 0.56983 / 0.27 (12795) hydrogen bonds : bond 0.04935 / 3.24 ( 571) hydrogen bonds : angle 4.34106 / 3.08 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.312 Fit side-chains REVERT: A 115 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7524 (p) REVERT: A 220 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8067 (mp) REVERT: B 115 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7584 (p) REVERT: B 206 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8128 (mm) REVERT: B 212 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7385 (mp) REVERT: C 115 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7511 (p) REVERT: C 206 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8172 (tp) REVERT: C 212 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7332 (mp) outliers start: 21 outliers final: 10 residues processed: 114 average time/residue: 0.3633 time to fit residues: 45.2760 Evaluate side-chains 121 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.093525 restraints weight = 9986.968| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.11 r_work: 0.2914 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9531 Z= 0.130 Angle : 0.528 8.209 12795 Z= 0.255 Chirality : 0.039 0.157 1428 Planarity : 0.005 0.044 1425 Dihedral : 17.206 179.886 1812 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.42 % Allowed : 8.19 % Favored : 89.39 % 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: 2.02 (0.25), residues: 1059 helix: 1.56 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 0.98 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.011 0.001 TYR B 369 PHE 0.013 0.001 PHE A 71 TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9531) covalent geometry : angle 0.52770 / 0.25 (12795) hydrogen bonds : bond 0.04560 / 2.99 ( 571) hydrogen bonds : angle 4.17551 / 2.96 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.195 Fit side-chains REVERT: A 115 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7510 (p) REVERT: A 220 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 115 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7591 (p) REVERT: B 212 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7372 (mp) REVERT: C 115 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7520 (p) REVERT: C 206 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8156 (tp) REVERT: C 212 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7377 (mp) outliers start: 21 outliers final: 8 residues processed: 112 average time/residue: 0.3844 time to fit residues: 46.9787 Evaluate side-chains 120 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.090629 restraints weight = 10104.450| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.13 r_work: 0.2848 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9531 Z= 0.191 Angle : 0.597 9.188 12795 Z= 0.286 Chirality : 0.043 0.165 1428 Planarity : 0.005 0.045 1425 Dihedral : 17.415 179.858 1812 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.65 % Allowed : 8.07 % Favored : 89.27 % 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: 1.87 (0.25), residues: 1059 helix: 1.42 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.03 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.013 0.002 TYR B 369 PHE 0.015 0.002 PHE C 288 TRP 0.010 0.001 TRP B 306 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 9531) covalent geometry : angle 0.59659 / 0.29 (12795) hydrogen bonds : bond 0.05168 / 3.39 ( 571) hydrogen bonds : angle 4.33070 / 3.07 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.269 Fit side-chains REVERT: A 220 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8054 (mp) REVERT: B 115 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7605 (p) REVERT: B 204 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (mp) REVERT: B 212 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7430 (mp) REVERT: C 206 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8206 (tp) REVERT: C 212 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7398 (mp) outliers start: 23 outliers final: 14 residues processed: 111 average time/residue: 0.4225 time to fit residues: 51.0728 Evaluate side-chains 121 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.093437 restraints weight = 9984.095| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.10 r_work: 0.2900 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9531 Z= 0.132 Angle : 0.534 8.451 12795 Z= 0.258 Chirality : 0.039 0.154 1428 Planarity : 0.005 0.043 1425 Dihedral : 16.858 179.580 1812 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.88 % Allowed : 7.84 % Favored : 89.27 % 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: 2.19 (0.25), residues: 1059 helix: 1.67 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.09 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.011 0.001 TYR B 369 PHE 0.014 0.001 PHE A 71 TRP 0.010 0.001 TRP B 306 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9531) covalent geometry : angle 0.53422 / 0.26 (12795) hydrogen bonds : bond 0.04601 / 3.01 ( 571) hydrogen bonds : angle 4.15884 / 2.95 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.317 Fit side-chains REVERT: A 115 SER cc_start: 0.7778 (OUTLIER) cc_final: 0.7438 (p) REVERT: A 220 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 256 MET cc_start: 0.8744 (mtp) cc_final: 0.8539 (mtm) REVERT: B 115 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7571 (p) REVERT: B 204 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7400 (mp) REVERT: B 212 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7357 (mp) REVERT: C 115 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7498 (p) REVERT: C 206 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8165 (tp) REVERT: C 212 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7350 (mp) outliers start: 25 outliers final: 11 residues processed: 116 average time/residue: 0.4105 time to fit residues: 51.9976 Evaluate side-chains 123 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.092815 restraints weight = 9956.197| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.10 r_work: 0.2880 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9531 Z= 0.144 Angle : 0.547 9.081 12795 Z= 0.263 Chirality : 0.040 0.157 1428 Planarity : 0.005 0.043 1425 Dihedral : 16.744 179.666 1812 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.65 % Allowed : 7.96 % Favored : 89.39 % 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: 2.19 (0.25), residues: 1059 helix: 1.66 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.11 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.012 0.001 TYR B 369 PHE 0.014 0.001 PHE A 71 TRP 0.010 0.001 TRP B 306 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9531) covalent geometry : angle 0.54661 / 0.26 (12795) hydrogen bonds : bond 0.04723 / 3.09 ( 571) hydrogen bonds : angle 4.17037 / 2.96 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.327 Fit side-chains REVERT: A 115 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7480 (p) REVERT: A 220 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 256 MET cc_start: 0.8779 (mtp) cc_final: 0.8567 (mtm) REVERT: B 115 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7607 (p) REVERT: B 204 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7414 (mp) REVERT: B 212 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7421 (mp) REVERT: C 206 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8161 (tp) REVERT: C 212 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7378 (mp) outliers start: 23 outliers final: 13 residues processed: 113 average time/residue: 0.4476 time to fit residues: 55.0016 Evaluate side-chains 125 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.093510 restraints weight = 9991.174| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.11 r_work: 0.2903 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9531 Z= 0.134 Angle : 0.536 8.827 12795 Z= 0.258 Chirality : 0.040 0.155 1428 Planarity : 0.005 0.043 1425 Dihedral : 16.498 179.191 1812 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.54 % Allowed : 8.30 % Favored : 89.16 % 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: 2.28 (0.25), residues: 1059 helix: 1.73 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.13 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.011 0.001 TYR B 369 PHE 0.014 0.001 PHE A 71 TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9531) covalent geometry : angle 0.53627 / 0.26 (12795) hydrogen bonds : bond 0.04601 / 3.01 ( 571) hydrogen bonds : angle 4.12723 / 2.93 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.305 Fit side-chains REVERT: A 115 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7466 (p) REVERT: A 220 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 115 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7556 (p) REVERT: B 204 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7342 (mp) REVERT: B 212 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7394 (mp) REVERT: C 115 SER cc_start: 0.7860 (OUTLIER) cc_final: 0.7511 (p) REVERT: C 206 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8141 (tp) REVERT: C 212 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7367 (mp) outliers start: 22 outliers final: 12 residues processed: 117 average time/residue: 0.3876 time to fit residues: 49.5985 Evaluate side-chains 124 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.093869 restraints weight = 9848.430| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.11 r_work: 0.2917 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 0.033 9531 Z= 0.132 Angle : 0.535 8.857 12795 Z= 0.258 Chirality : 0.040 0.154 1428 Planarity : 0.005 0.042 1425 Dihedral : 16.334 179.319 1812 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.65 % Allowed : 8.65 % Favored : 88.70 % 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: 2.33 (0.25), residues: 1059 helix: 1.77 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.16 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.012 0.001 TYR B 369 PHE 0.012 0.001 PHE C 71 TRP 0.011 0.001 TRP B 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9531) covalent geometry : angle 0.53535 / 0.26 (12795) hydrogen bonds : bond 0.04586 / 3.00 ( 571) hydrogen bonds : angle 4.11141 / 2.92 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.253 Fit side-chains REVERT: A 115 SER cc_start: 0.7782 (OUTLIER) cc_final: 0.7458 (p) REVERT: A 220 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 297 MET cc_start: 0.8869 (mmm) cc_final: 0.8457 (mmm) REVERT: B 115 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7568 (p) REVERT: B 204 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7297 (mp) REVERT: B 212 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7374 (mp) REVERT: C 115 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7503 (p) REVERT: C 206 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8147 (tp) REVERT: C 212 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7361 (mp) outliers start: 23 outliers final: 11 residues processed: 116 average time/residue: 0.4286 time to fit residues: 54.2651 Evaluate side-chains 125 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 0.0000 chunk 99 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.095622 restraints weight = 9888.578| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.11 r_work: 0.2944 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9531 Z= 0.116 Angle : 0.515 8.633 12795 Z= 0.249 Chirality : 0.039 0.153 1428 Planarity : 0.004 0.042 1425 Dihedral : 15.925 178.935 1812 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.31 % Allowed : 8.88 % Favored : 88.81 % 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: 2.49 (0.26), residues: 1059 helix: 1.90 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.17 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.011 0.001 TYR B 369 PHE 0.013 0.001 PHE C 71 TRP 0.014 0.001 TRP B 171 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9531) covalent geometry : angle 0.51517 / 0.25 (12795) hydrogen bonds : bond 0.04374 / 2.86 ( 571) hydrogen bonds : angle 4.03156 / 2.86 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.215 Fit side-chains REVERT: A 115 SER cc_start: 0.7770 (OUTLIER) cc_final: 0.7392 (p) REVERT: A 256 MET cc_start: 0.8695 (mtp) cc_final: 0.8472 (mtm) REVERT: A 297 MET cc_start: 0.8884 (mmm) cc_final: 0.8466 (mmm) REVERT: B 115 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7560 (p) REVERT: B 204 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7276 (mp) REVERT: B 212 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7347 (mp) REVERT: C 115 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7507 (p) REVERT: C 206 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8137 (tp) outliers start: 20 outliers final: 10 residues processed: 116 average time/residue: 0.3999 time to fit residues: 50.5993 Evaluate side-chains 122 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 357 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 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 = 0.3325 r_free = 0.3325 target = 0.117323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.094808 restraints weight = 9910.621| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.11 r_work: 0.2932 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9531 Z= 0.124 Angle : 0.527 8.868 12795 Z= 0.254 Chirality : 0.039 0.152 1428 Planarity : 0.005 0.042 1425 Dihedral : 15.891 178.789 1812 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.31 % Allowed : 9.11 % Favored : 88.58 % 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: 2.48 (0.25), residues: 1059 helix: 1.88 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.18 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.012 0.001 TYR B 369 PHE 0.014 0.001 PHE A 71 TRP 0.016 0.001 TRP B 171 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9531) covalent geometry : angle 0.52674 / 0.25 (12795) hydrogen bonds : bond 0.04481 / 2.93 ( 571) hydrogen bonds : angle 4.05544 / 2.88 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.10 seconds wall clock time: 46 minutes 22.59 seconds (2782.59 seconds total)