Starting phenix.real_space_refine on Fri Feb 14 07:13:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8blp_16112/02_2025/8blp_16112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blp_16112/02_2025/8blp_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_16112/02_2025/8blp_16112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blp_16112/02_2025/8blp_16112.map" model { file = "/net/cci-nas-00/data/ceres_data/8blp_16112/02_2025/8blp_16112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blp_16112/02_2025/8blp_16112.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 819 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: 819 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: 819 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: 6.16, per 1000 atoms: 0.66 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.88 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: 2.63 Time building geometry restraints manager: 2.96 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: 5638 34.69 - 69.39: 371 69.39 - 104.08: 9 104.08 - 138.77: 3 138.77 - 173.47: 3 Dihedral angle restraints: 6024 sinusoidal: 2970 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 6021 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: 0.03 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.860 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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= 0.590 Angle : 1.371 16.505 12795 Z= 0.543 Chirality : 0.049 0.163 1428 Planarity : 0.008 0.095 1425 Dihedral : 19.492 173.468 4068 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (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 TRP 0.011 0.002 TRP C 306 HIS 0.005 0.001 HIS B 259 PHE 0.017 0.002 PHE C 288 TYR 0.014 0.002 TYR B 234 ARG 0.002 0.001 ARG C 114 *********************** 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 : 0.921 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: 1.1170 time to fit residues: 130.8983 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 : 0.983 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3297 r_free = 0.3297 target = 0.115270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.093350 restraints weight = 9972.016| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.09 r_work: 0.2910 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1102 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= 0.181 Angle : 0.556 7.977 12795 Z= 0.267 Chirality : 0.039 0.156 1428 Planarity : 0.005 0.046 1425 Dihedral : 18.931 177.023 2330 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.54 % Allowed : 6.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1059 helix: 0.62 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 0.60 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 306 HIS 0.003 0.001 HIS A 259 PHE 0.014 0.001 PHE A 71 TYR 0.012 0.001 TYR B 369 ARG 0.001 0.000 ARG C 374 *********************** 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: 22 poor density : 109 time to evaluate : 0.882 Fit side-chains REVERT: A 115 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7574 (p) REVERT: A 220 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8013 (mp) REVERT: B 115 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7679 (p) REVERT: B 206 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8134 (mm) REVERT: C 115 SER cc_start: 0.7852 (OUTLIER) cc_final: 0.7559 (p) REVERT: C 212 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7357 (mp) outliers start: 22 outliers final: 7 residues processed: 116 average time/residue: 0.9667 time to fit residues: 122.3629 Evaluate side-chains 115 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 21 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3287 r_free = 0.3287 target = 0.114489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.092207 restraints weight = 9935.993| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.10 r_work: 0.2883 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 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 = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9531 Z= 0.219 Angle : 0.562 8.699 12795 Z= 0.270 Chirality : 0.041 0.159 1428 Planarity : 0.005 0.045 1425 Dihedral : 16.510 179.509 2328 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.31 % Allowed : 7.61 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1059 helix: 1.23 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 0.86 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 306 HIS 0.004 0.001 HIS B 259 PHE 0.014 0.002 PHE C 288 TYR 0.013 0.001 TYR C 369 ARG 0.001 0.000 ARG C 114 *********************** 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 130 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.886 Fit side-chains REVERT: A 115 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7527 (p) REVERT: A 220 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 115 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7586 (p) REVERT: B 206 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8130 (mm) REVERT: B 212 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7386 (mp) REVERT: C 115 SER cc_start: 0.7893 (OUTLIER) cc_final: 0.7559 (p) REVERT: C 206 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8177 (tp) REVERT: C 212 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7331 (mp) outliers start: 20 outliers final: 10 residues processed: 117 average time/residue: 1.0316 time to fit residues: 131.3041 Evaluate side-chains 124 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.091368 restraints weight = 9935.447| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.10 r_work: 0.2841 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9531 Z= 0.251 Angle : 0.579 8.891 12795 Z= 0.278 Chirality : 0.042 0.163 1428 Planarity : 0.005 0.046 1425 Dihedral : 15.798 179.995 2328 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.65 % Allowed : 7.73 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1059 helix: 1.39 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 0.96 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 306 HIS 0.005 0.001 HIS A 259 PHE 0.015 0.002 PHE B 288 TYR 0.013 0.001 TYR B 369 ARG 0.001 0.000 ARG C 114 *********************** 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 126 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.905 Fit side-chains REVERT: A 115 SER cc_start: 0.7828 (OUTLIER) cc_final: 0.7539 (p) REVERT: A 220 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 115 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7625 (p) REVERT: B 204 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7459 (mp) REVERT: B 206 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 212 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7424 (mp) REVERT: C 206 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8210 (tp) REVERT: C 212 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7393 (mp) outliers start: 23 outliers final: 11 residues processed: 109 average time/residue: 1.0325 time to fit residues: 122.8600 Evaluate side-chains 120 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 204 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.094732 restraints weight = 9869.301| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.09 r_work: 0.2933 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 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 = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9531 Z= 0.161 Angle : 0.518 8.088 12795 Z= 0.249 Chirality : 0.039 0.153 1428 Planarity : 0.004 0.044 1425 Dihedral : 15.063 179.565 2328 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.54 % Allowed : 8.42 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.26), residues: 1059 helix: 1.73 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.05 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE C 71 TYR 0.011 0.001 TYR A 369 ARG 0.001 0.000 ARG C 114 *********************** 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 129 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.962 Fit side-chains REVERT: A 115 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7479 (p) REVERT: B 115 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7551 (p) REVERT: B 212 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7335 (mp) REVERT: C 115 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.7492 (p) REVERT: C 206 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8150 (tp) outliers start: 22 outliers final: 9 residues processed: 115 average time/residue: 1.0445 time to fit residues: 131.2235 Evaluate side-chains 118 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 77 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.092629 restraints weight = 9911.505| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.10 r_work: 0.2889 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9531 Z= 0.220 Angle : 0.557 9.351 12795 Z= 0.267 Chirality : 0.041 0.157 1428 Planarity : 0.005 0.044 1425 Dihedral : 15.111 179.868 2328 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 8.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (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 TRP 0.009 0.001 TRP B 306 HIS 0.005 0.001 HIS A 259 PHE 0.014 0.001 PHE A 71 TYR 0.012 0.001 TYR B 369 ARG 0.001 0.000 ARG C 114 *********************** 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 130 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.000 Fit side-chains REVERT: A 115 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7502 (p) REVERT: A 220 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 256 MET cc_start: 0.8839 (mtp) cc_final: 0.8587 (mtm) REVERT: B 115 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7605 (p) REVERT: B 212 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7403 (mp) REVERT: C 206 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8160 (tp) REVERT: C 212 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7356 (mp) outliers start: 24 outliers final: 14 residues processed: 118 average time/residue: 1.0251 time to fit residues: 131.7304 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 : 0.931 ------------------------------------------------------------------------------- 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 175 VAL 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 175 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.091425 restraints weight = 10056.423| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.12 r_work: 0.2862 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 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 = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9531 Z= 0.255 Angle : 0.581 9.434 12795 Z= 0.278 Chirality : 0.042 0.161 1428 Planarity : 0.005 0.044 1425 Dihedral : 15.189 179.746 2328 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.88 % Allowed : 8.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.25), residues: 1059 helix: 1.56 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.13 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 306 HIS 0.005 0.001 HIS A 259 PHE 0.014 0.002 PHE A 288 TYR 0.013 0.001 TYR B 369 ARG 0.001 0.000 ARG C 114 *********************** 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 128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.950 Fit side-chains REVERT: A 115 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7491 (p) REVERT: A 220 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 256 MET cc_start: 0.8818 (mtp) cc_final: 0.8597 (mtm) REVERT: B 115 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7607 (p) REVERT: B 204 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7359 (mp) REVERT: B 212 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7415 (mp) REVERT: C 206 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8172 (tp) REVERT: C 212 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7373 (mp) outliers start: 25 outliers final: 15 residues processed: 113 average time/residue: 1.0403 time to fit residues: 128.2346 Evaluate side-chains 124 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 175 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 175 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 83 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.094194 restraints weight = 10123.264| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.11 r_work: 0.2892 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 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 = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1667 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= 0.174 Angle : 0.529 8.683 12795 Z= 0.255 Chirality : 0.039 0.153 1428 Planarity : 0.005 0.044 1425 Dihedral : 14.671 179.470 2328 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.42 % Allowed : 8.65 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.25), residues: 1059 helix: 1.79 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.16 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 306 HIS 0.005 0.001 HIS A 259 PHE 0.015 0.001 PHE A 71 TYR 0.011 0.001 TYR B 369 ARG 0.001 0.000 ARG C 114 *********************** 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 131 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.968 Fit side-chains REVERT: A 115 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7493 (p) REVERT: A 297 MET cc_start: 0.8935 (mmm) cc_final: 0.8505 (mmm) REVERT: B 115 SER cc_start: 0.7954 (OUTLIER) cc_final: 0.7594 (p) REVERT: B 212 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7379 (mp) REVERT: C 115 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7529 (p) REVERT: C 206 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8188 (tp) REVERT: C 212 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7334 (mp) outliers start: 21 outliers final: 11 residues processed: 120 average time/residue: 1.0220 time to fit residues: 133.7066 Evaluate side-chains 123 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 129 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 206 ILE 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 80 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.094068 restraints weight = 9927.691| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.11 r_work: 0.2911 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 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 = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9531 Z= 0.181 Angle : 0.536 8.845 12795 Z= 0.258 Chirality : 0.040 0.154 1428 Planarity : 0.005 0.044 1425 Dihedral : 14.500 179.381 2328 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.42 % Allowed : 9.11 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.25), residues: 1059 helix: 1.81 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.16 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 171 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE C 71 TYR 0.012 0.001 TYR A 369 ARG 0.001 0.000 ARG C 114 *********************** 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 128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.909 Fit side-chains REVERT: A 115 SER cc_start: 0.7781 (OUTLIER) cc_final: 0.7402 (p) REVERT: B 115 SER cc_start: 0.7978 (OUTLIER) cc_final: 0.7590 (p) REVERT: B 204 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7289 (mp) REVERT: B 212 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7369 (mp) REVERT: C 115 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7502 (p) REVERT: C 206 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8148 (tp) REVERT: C 212 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7330 (mp) outliers start: 21 outliers final: 11 residues processed: 115 average time/residue: 1.0312 time to fit residues: 129.0907 Evaluate side-chains 125 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 175 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 3 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.093763 restraints weight = 9997.893| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.10 r_work: 0.2896 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 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 = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1693 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= 0.194 Angle : 0.544 8.944 12795 Z= 0.262 Chirality : 0.040 0.155 1428 Planarity : 0.005 0.044 1425 Dihedral : 14.436 179.116 2328 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.42 % Allowed : 9.34 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.25), residues: 1059 helix: 1.78 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.16 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 171 HIS 0.005 0.001 HIS A 259 PHE 0.013 0.001 PHE C 71 TYR 0.012 0.001 TYR C 369 ARG 0.001 0.000 ARG C 114 ********************** 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: 21 poor density : 107 time to evaluate : 0.916 Fit side-chains REVERT: A 115 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7421 (p) REVERT: B 115 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7602 (p) REVERT: B 204 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7322 (mp) REVERT: B 212 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7389 (mp) REVERT: C 206 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8166 (tp) REVERT: C 212 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7354 (mp) outliers start: 21 outliers final: 12 residues processed: 115 average time/residue: 1.0515 time to fit residues: 131.8602 Evaluate side-chains 125 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 175 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 67 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.095246 restraints weight = 9922.805| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.11 r_work: 0.2930 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 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 = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1812 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= 0.163 Angle : 0.525 8.676 12795 Z= 0.253 Chirality : 0.039 0.151 1428 Planarity : 0.005 0.044 1425 Dihedral : 14.174 179.037 2328 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.31 % Allowed : 9.57 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.25), residues: 1059 helix: 1.89 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.16 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 171 HIS 0.004 0.001 HIS A 259 PHE 0.013 0.001 PHE C 71 TYR 0.011 0.001 TYR B 369 ARG 0.001 0.000 ARG C 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5948.55 seconds wall clock time: 106 minutes 8.60 seconds (6368.60 seconds total)