Starting phenix.real_space_refine on Wed Sep 25 08:21:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blp_16112/09_2024/8blp_16112.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blp_16112/09_2024/8blp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blp_16112/09_2024/8blp_16112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blp_16112/09_2024/8blp_16112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blp_16112/09_2024/8blp_16112.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blp_16112/09_2024/8blp_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-5461/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: 6.71, per 1000 atoms: 0.72 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: 2.57 Conformation dependent library (CDL) restraints added in 1.0 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: 0.98 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: 2.51 Time building geometry restraints manager: 2.90 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: 0.00 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 24.780 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.810 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.968 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: 1.0671 time to fit residues: 125.0547 Evaluate side-chains 103 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.072 Fit side-chains REVERT: A 115 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7794 (p) REVERT: A 220 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8082 (mp) REVERT: B 115 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7865 (p) REVERT: B 204 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7528 (mt) REVERT: B 206 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8177 (mm) REVERT: C 115 SER cc_start: 0.8012 (OUTLIER) cc_final: 0.7737 (p) REVERT: C 212 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7513 (mp) outliers start: 22 outliers final: 7 residues processed: 116 average time/residue: 0.9499 time to fit residues: 120.3459 Evaluate side-chains 116 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 94 optimal weight: 0.0020 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.4506 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9531 Z= 0.143 Angle : 0.507 7.412 12795 Z= 0.244 Chirality : 0.038 0.152 1428 Planarity : 0.004 0.043 1425 Dihedral : 15.811 179.290 2328 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.19 % Allowed : 7.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.25), residues: 1059 helix: 1.52 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 0.93 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.003 0.001 HIS A 259 PHE 0.011 0.001 PHE C 288 TYR 0.011 0.001 TYR A 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 132 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.985 Fit side-chains REVERT: A 115 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7714 (p) REVERT: B 115 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7795 (p) REVERT: B 204 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7438 (mp) REVERT: B 212 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7443 (mp) REVERT: C 115 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7718 (p) REVERT: C 206 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8222 (tp) outliers start: 19 outliers final: 7 residues processed: 118 average time/residue: 1.0464 time to fit residues: 133.8382 Evaluate side-chains 116 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 206 ILE 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 94 optimal weight: 0.0770 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1624 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= 0.166 Angle : 0.529 7.950 12795 Z= 0.253 Chirality : 0.039 0.154 1428 Planarity : 0.004 0.044 1425 Dihedral : 15.242 179.991 2328 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.54 % Allowed : 8.65 % 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 (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: 2.26 (0.26), residues: 1059 helix: 1.74 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.03 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 306 HIS 0.004 0.001 HIS A 259 PHE 0.013 0.001 PHE C 288 TYR 0.012 0.001 TYR B 369 ARG 0.000 0.000 ARG A 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 128 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.053 Fit side-chains REVERT: A 115 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7687 (p) REVERT: A 220 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 115 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7784 (p) REVERT: B 204 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7434 (mp) REVERT: B 212 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7454 (mp) REVERT: C 115 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7713 (p) REVERT: C 206 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8245 (tp) REVERT: C 212 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7399 (mp) outliers start: 22 outliers final: 8 residues processed: 113 average time/residue: 1.0561 time to fit residues: 129.6746 Evaluate side-chains 121 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 70 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1694 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= 0.167 Angle : 0.526 7.838 12795 Z= 0.252 Chirality : 0.039 0.152 1428 Planarity : 0.004 0.042 1425 Dihedral : 14.863 179.898 2328 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.54 % Allowed : 8.65 % 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 (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: 2.42 (0.26), residues: 1059 helix: 1.85 (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 0.008 0.001 TRP B 306 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE C 288 TYR 0.011 0.001 TYR A 369 ARG 0.001 0.000 ARG A 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 fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.928 Fit side-chains REVERT: A 115 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7599 (p) REVERT: B 115 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7756 (p) REVERT: B 204 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7399 (mp) REVERT: B 212 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7465 (mp) REVERT: C 115 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7710 (p) REVERT: C 206 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8221 (tp) REVERT: C 212 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7411 (mp) outliers start: 22 outliers final: 8 residues processed: 115 average time/residue: 1.0301 time to fit residues: 128.8195 Evaluate side-chains 122 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1757 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= 0.162 Angle : 0.523 8.016 12795 Z= 0.250 Chirality : 0.039 0.152 1428 Planarity : 0.004 0.042 1425 Dihedral : 14.657 179.924 2328 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 2.51 (0.26), residues: 1059 helix: 1.91 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.17 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 306 HIS 0.004 0.001 HIS A 259 PHE 0.012 0.001 PHE A 71 TYR 0.011 0.001 TYR B 369 ARG 0.001 0.000 ARG B 374 *********************** 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 fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.983 Fit side-chains REVERT: A 115 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7591 (p) REVERT: A 220 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 256 MET cc_start: 0.8822 (mtp) cc_final: 0.8615 (mtm) REVERT: A 297 MET cc_start: 0.9005 (mmm) cc_final: 0.8453 (mmm) REVERT: B 115 SER cc_start: 0.8113 (OUTLIER) cc_final: 0.7745 (p) REVERT: B 204 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7413 (mp) REVERT: B 212 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7464 (mp) REVERT: C 115 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7693 (p) REVERT: C 206 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8229 (tp) REVERT: C 212 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7407 (mp) outliers start: 22 outliers final: 8 residues processed: 118 average time/residue: 1.0131 time to fit residues: 130.0537 Evaluate side-chains 123 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1626 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= 0.218 Angle : 0.559 9.183 12795 Z= 0.267 Chirality : 0.041 0.157 1428 Planarity : 0.004 0.043 1425 Dihedral : 14.819 179.722 2328 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.54 % Allowed : 8.88 % 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: 2.33 (0.25), residues: 1059 helix: 1.76 (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 0.009 0.001 TRP B 171 HIS 0.004 0.001 HIS A 259 PHE 0.013 0.001 PHE A 288 TYR 0.012 0.001 TYR B 369 ARG 0.001 0.000 ARG B 374 *********************** 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 fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 0.972 Fit side-chains REVERT: A 115 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7653 (p) REVERT: A 220 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8131 (mp) REVERT: B 115 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7727 (p) REVERT: B 204 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7479 (mp) REVERT: B 212 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7487 (mp) REVERT: C 115 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7673 (p) REVERT: C 206 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8274 (tp) REVERT: C 212 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7434 (mp) outliers start: 22 outliers final: 10 residues processed: 115 average time/residue: 1.0118 time to fit residues: 126.7051 Evaluate side-chains 124 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1608 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= 0.226 Angle : 0.566 9.128 12795 Z= 0.271 Chirality : 0.041 0.158 1428 Planarity : 0.005 0.043 1425 Dihedral : 14.829 179.630 2328 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.65 % Allowed : 8.77 % 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: 2.25 (0.25), residues: 1059 helix: 1.70 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.15 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 171 HIS 0.005 0.001 HIS A 259 PHE 0.014 0.001 PHE A 288 TYR 0.013 0.001 TYR C 369 ARG 0.001 0.000 ARG B 374 *********************** 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 128 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.012 Fit side-chains REVERT: A 115 SER cc_start: 0.7981 (OUTLIER) cc_final: 0.7647 (p) REVERT: A 220 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8130 (mp) REVERT: B 115 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7747 (p) REVERT: B 204 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 212 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7490 (mp) REVERT: C 115 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7670 (p) REVERT: C 206 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8272 (tp) REVERT: C 212 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7449 (mp) outliers start: 23 outliers final: 12 residues processed: 114 average time/residue: 1.0787 time to fit residues: 133.7856 Evaluate side-chains 124 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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= 0.157 Angle : 0.522 8.602 12795 Z= 0.250 Chirality : 0.039 0.153 1428 Planarity : 0.004 0.042 1425 Dihedral : 14.299 179.843 2328 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.19 % Allowed : 9.23 % 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: 2.52 (0.26), residues: 1059 helix: 1.92 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.18 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.005 0.001 HIS A 259 PHE 0.013 0.001 PHE C 71 TYR 0.011 0.001 TYR C 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 127 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.027 Fit side-chains REVERT: A 115 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7550 (p) REVERT: A 256 MET cc_start: 0.8856 (mtp) cc_final: 0.8622 (mtm) REVERT: A 297 MET cc_start: 0.8956 (mmm) cc_final: 0.8569 (mmm) REVERT: B 115 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7723 (p) REVERT: B 204 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7381 (mp) REVERT: B 212 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7454 (mp) REVERT: C 115 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7687 (p) REVERT: C 206 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8215 (tp) REVERT: C 212 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7412 (mp) outliers start: 19 outliers final: 7 residues processed: 115 average time/residue: 1.0130 time to fit residues: 126.6988 Evaluate side-chains 121 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 C residue 115 SER 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 99 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1752 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= 0.190 Angle : 0.546 9.040 12795 Z= 0.261 Chirality : 0.040 0.155 1428 Planarity : 0.004 0.042 1425 Dihedral : 14.360 179.665 2328 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.85 % Allowed : 9.57 % 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: 2.41 (0.25), residues: 1059 helix: 1.83 (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 A 71 TYR 0.012 0.001 TYR B 369 ARG 0.001 0.000 ARG B 374 ********************** 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 123 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.986 Fit side-chains REVERT: A 115 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7551 (p) REVERT: A 297 MET cc_start: 0.8956 (mmm) cc_final: 0.8670 (mmm) REVERT: B 115 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7748 (p) REVERT: B 204 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7390 (mp) REVERT: B 212 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7459 (mp) REVERT: C 115 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7680 (p) REVERT: C 206 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8231 (tp) REVERT: C 212 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7431 (mp) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 1.0741 time to fit residues: 132.5532 Evaluate side-chains 121 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 C residue 115 SER 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 88 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.118090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095798 restraints weight = 9816.281| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.10 r_work: 0.2923 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1854 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= 0.162 Angle : 0.526 8.833 12795 Z= 0.252 Chirality : 0.039 0.154 1428 Planarity : 0.004 0.042 1425 Dihedral : 14.110 179.291 2328 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 9.57 % 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: 2.52 (0.25), residues: 1059 helix: 1.92 (0.17), residues: 780 sheet: None (None), residues: 0 loop : 1.18 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 171 HIS 0.005 0.001 HIS A 259 PHE 0.013 0.001 PHE C 71 TYR 0.011 0.001 TYR C 369 ARG 0.001 0.000 ARG B 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2977.40 seconds wall clock time: 53 minutes 42.35 seconds (3222.35 seconds total)