Starting phenix.real_space_refine on Thu Jul 2 08:02:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sfk_25091/07_2026/7sfk_25091.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sfk_25091/07_2026/7sfk_25091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sfk_25091/07_2026/7sfk_25091.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sfk_25091/07_2026/7sfk_25091.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sfk_25091/07_2026/7sfk_25091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sfk_25091/07_2026/7sfk_25091.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sfk_25091/07_2026/7sfk_25091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sfk_25091/07_2026/7sfk_25091.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.202 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 3 5.49 5 S 48 5.16 5 C 4971 2.51 5 N 1098 2.21 5 O 1299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7419 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 155 Unusual residues: {'PEE': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PEE:plan-2': 3, 'PEE:plan-1': 5, 'RET:plan-5': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Unusual residues: {'PEE': 6, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PEE:plan-2': 2, 'PEE:plan-1': 4, 'RET:plan-5': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 164 Unusual residues: {'PEE': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PEE:plan-1': 6, 'PEE:plan-2': 4, 'RET:plan-5': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 1.47, per 1000 atoms: 0.20 Number of scatterers: 7419 At special positions: 0 Unit cell: (78.453, 79.59, 88.686, 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 48 16.00 P 3 15.00 O 1299 8.00 N 1098 7.00 C 4971 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 320.1 milliseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 26 through 53 Processing helix chain 'A' and resid 63 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 72 through 95 removed outlier: 3.510A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.881A pdb=" N THR A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Proline residue: A 121 - end of helix removed outlier: 3.610A pdb=" N GLN A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 158 removed outlier: 3.832A pdb=" N CYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 164 through 200 removed outlier: 4.025A pdb=" N TYR A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.736A pdb=" N HIS A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 241 through 269 removed outlier: 3.601A pdb=" N GLU A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.705A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 26 through 53 Processing helix chain 'B' and resid 63 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 72 through 95 removed outlier: 3.511A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.881A pdb=" N THR B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Proline residue: B 121 - end of helix removed outlier: 3.610A pdb=" N GLN B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 158 removed outlier: 3.831A pdb=" N CYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 164 through 200 removed outlier: 4.026A pdb=" N TYR B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.736A pdb=" N HIS B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 241 through 269 removed outlier: 3.600A pdb=" N GLU B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 removed outlier: 3.706A pdb=" N GLY B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 53 Processing helix chain 'C' and resid 63 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 72 through 95 removed outlier: 3.510A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 removed outlier: 3.881A pdb=" N THR C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Proline residue: C 121 - end of helix removed outlier: 3.610A pdb=" N GLN C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 158 removed outlier: 3.832A pdb=" N CYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 164 through 200 removed outlier: 4.025A pdb=" N TYR C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.736A pdb=" N HIS C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 241 through 269 removed outlier: 3.600A pdb=" N GLU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.706A pdb=" N GLY C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2059 1.34 - 1.45: 1517 1.45 - 1.57: 3918 1.57 - 1.69: 3 1.69 - 1.81: 75 Bond restraints: 7572 Sorted by residual: bond pdb=" C30 PEE B 404 " pdb=" O5 PEE B 404 " ideal model delta sigma weight residual 1.206 1.353 -0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C30 PEE A 404 " pdb=" O5 PEE A 404 " ideal model delta sigma weight residual 1.206 1.353 -0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" C30 PEE C 405 " pdb=" O5 PEE C 405 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C30 PEE B 402 " pdb=" O5 PEE B 402 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C30 PEE C 403 " pdb=" O5 PEE C 403 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.33e+01 ... (remaining 7567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 9808 2.45 - 4.90: 315 4.90 - 7.34: 20 7.34 - 9.79: 15 9.79 - 12.24: 9 Bond angle restraints: 10167 Sorted by residual: angle pdb=" C11 PEE C 402 " pdb=" C10 PEE C 402 " pdb=" O2 PEE C 402 " ideal model delta sigma weight residual 111.70 123.94 -12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C11 PEE B 401 " pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 111.70 123.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C11 PEE A 401 " pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 111.70 123.92 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" C31 PEE B 404 " pdb=" C30 PEE B 404 " pdb=" O3 PEE B 404 " ideal model delta sigma weight residual 111.87 123.95 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C31 PEE A 404 " pdb=" C30 PEE A 404 " pdb=" O3 PEE A 404 " ideal model delta sigma weight residual 111.87 123.91 -12.04 3.00e+00 1.11e-01 1.61e+01 ... (remaining 10162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 4176 35.68 - 71.36: 90 71.36 - 107.04: 12 107.04 - 142.72: 6 142.72 - 178.40: 6 Dihedral angle restraints: 4290 sinusoidal: 1815 harmonic: 2475 Sorted by residual: dihedral pdb=" C32 PEE C 404 " pdb=" C30 PEE C 404 " pdb=" C31 PEE C 404 " pdb=" O3 PEE C 404 " ideal model delta sinusoidal sigma weight residual 161.16 -20.44 -178.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C32 PEE B 403 " pdb=" C30 PEE B 403 " pdb=" C31 PEE B 403 " pdb=" O3 PEE B 403 " ideal model delta sinusoidal sigma weight residual 161.16 -20.49 -178.35 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C32 PEE A 403 " pdb=" C30 PEE A 403 " pdb=" C31 PEE A 403 " pdb=" O3 PEE A 403 " ideal model delta sinusoidal sigma weight residual 161.16 -20.54 -178.30 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 633 0.033 - 0.065: 282 0.065 - 0.098: 78 0.098 - 0.130: 15 0.130 - 0.163: 3 Chirality restraints: 1011 Sorted by residual: chirality pdb=" C2 PEE A 406 " pdb=" C1 PEE A 406 " pdb=" C3 PEE A 406 " pdb=" O2 PEE A 406 " both_signs ideal model delta sigma weight residual False -2.33 -2.49 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" C2 PEE B 406 " pdb=" C1 PEE B 406 " pdb=" C3 PEE B 406 " pdb=" O2 PEE B 406 " both_signs ideal model delta sigma weight residual False -2.33 -2.49 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" C2 PEE C 408 " pdb=" C1 PEE C 408 " pdb=" C3 PEE C 408 " pdb=" O2 PEE C 408 " both_signs ideal model delta sigma weight residual False -2.33 -2.48 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1008 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 160 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 161 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 160 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 161 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 160 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 161 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 161 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 161 " -0.028 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1868 2.79 - 3.32: 6599 3.32 - 3.85: 12571 3.85 - 4.37: 15095 4.37 - 4.90: 26074 Nonbonded interactions: 62207 Sorted by model distance: nonbonded pdb=" O GLY C 107 " pdb=" O HOH C 501 " model vdw 2.265 3.040 nonbonded pdb=" O GLY B 107 " pdb=" O HOH B 501 " model vdw 2.273 3.040 nonbonded pdb=" O GLY A 107 " pdb=" O HOH A 501 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN A 110 " pdb=" O HOH A 502 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASN B 110 " pdb=" O HOH B 502 " model vdw 2.323 3.040 ... (remaining 62202 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 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 45 or name C46 or name C47)))) selection = (chain 'B' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or (resid 406 and (name C36 or name C37 or name C38 o \ r name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C \ 45 or name C46 or name C47)))) selection = (chain 'C' and (resid 2 through 285 or (resid 403 through 404 and (name C30 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name O3 or name O \ 5 )) or (resid 405 and (name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or resid 406)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.630 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.008 0.147 7575 Z= 0.387 Angle : 0.966 12.239 10167 Z= 0.401 Chirality : 0.039 0.163 1011 Planarity : 0.005 0.050 1242 Dihedral : 18.019 178.399 2724 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.43 % Allowed : 1.71 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.28), residues: 843 helix: 1.80 (0.20), residues: 576 sheet: None (None), residues: 0 loop : 1.31 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.013 0.002 TYR B 271 PHE 0.016 0.001 PHE B 176 TRP 0.009 0.001 TRP A 177 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.39 ( 7572) covalent geometry : angle 0.96555 / 0.40 (10167) hydrogen bonds : bond 0.14819 / 9.75 ( 450) hydrogen bonds : angle 4.67821 / 3.38 ( 1323) Misc. bond : bond 0.00059 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.158 Fit side-chains REVERT: A 68 GLN cc_start: 0.8415 (mp10) cc_final: 0.8188 (mp10) REVERT: A 148 MET cc_start: 0.7948 (ttp) cc_final: 0.7508 (ttp) REVERT: A 180 PHE cc_start: 0.8039 (t80) cc_final: 0.7823 (t80) REVERT: B 148 MET cc_start: 0.7888 (ttp) cc_final: 0.7637 (ttp) REVERT: C 148 MET cc_start: 0.8100 (ttp) cc_final: 0.7876 (ttp) outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.4231 time to fit residues: 45.5431 Evaluate side-chains 81 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN B 192 GLN C 9 GLN C 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118711 restraints weight = 7187.861| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.24 r_work: 0.3118 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7575 Z= 0.120 Angle : 0.473 4.991 10167 Z= 0.252 Chirality : 0.038 0.125 1011 Planarity : 0.004 0.045 1242 Dihedral : 15.287 142.320 1271 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.29), residues: 843 helix: 2.24 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 1.82 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 268 TYR 0.013 0.001 TYR B 271 PHE 0.013 0.002 PHE C 173 TRP 0.014 0.001 TRP A 19 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7572) covalent geometry : angle 0.47332 / 0.25 (10167) hydrogen bonds : bond 0.05370 / 3.60 ( 450) hydrogen bonds : angle 3.37537 / 2.43 ( 1323) Misc. bond : bond 0.00036 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.220 Fit side-chains REVERT: A 59 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7446 (mmtm) REVERT: A 68 GLN cc_start: 0.8098 (mp10) cc_final: 0.7597 (mp10) REVERT: A 148 MET cc_start: 0.8475 (ttp) cc_final: 0.8109 (ttp) REVERT: A 221 MET cc_start: 0.7212 (tmm) cc_final: 0.6947 (tmm) REVERT: A 277 ARG cc_start: 0.6653 (ptp90) cc_final: 0.6423 (ptp90) REVERT: B 148 MET cc_start: 0.8292 (ttp) cc_final: 0.8079 (ttp) REVERT: B 272 ASP cc_start: 0.7125 (p0) cc_final: 0.6750 (p0) outliers start: 6 outliers final: 4 residues processed: 101 average time/residue: 0.4013 time to fit residues: 43.3282 Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 ASN C 9 GLN C 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115990 restraints weight = 7087.008| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 0.97 r_work: 0.3054 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7575 Z= 0.238 Angle : 0.620 5.664 10167 Z= 0.329 Chirality : 0.045 0.125 1011 Planarity : 0.005 0.053 1242 Dihedral : 15.146 116.300 1269 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 8.55 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.28), residues: 843 helix: 1.77 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 1.35 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 268 TYR 0.027 0.002 TYR A 271 PHE 0.040 0.003 PHE C 155 TRP 0.019 0.002 TRP C 19 HIS 0.008 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 ( 7572) covalent geometry : angle 0.62032 / 0.33 (10167) hydrogen bonds : bond 0.07499 / 5.02 ( 450) hydrogen bonds : angle 3.72645 / 2.68 ( 1323) Misc. bond : bond 0.00027 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.276 Fit side-chains REVERT: A 59 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7433 (mmtm) REVERT: A 68 GLN cc_start: 0.8242 (mp10) cc_final: 0.7651 (mp10) REVERT: A 118 LEU cc_start: 0.8777 (tp) cc_final: 0.8530 (mt) REVERT: A 148 MET cc_start: 0.8371 (ttp) cc_final: 0.8048 (ttp) REVERT: A 221 MET cc_start: 0.7114 (tmm) cc_final: 0.6864 (tmm) REVERT: A 272 ASP cc_start: 0.7334 (p0) cc_final: 0.7070 (p0) REVERT: B 9 GLN cc_start: 0.8210 (tt0) cc_final: 0.7897 (tt0) REVERT: B 272 ASP cc_start: 0.7677 (p0) cc_final: 0.7295 (p0) REVERT: C 221 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.7023 (tmm) outliers start: 13 outliers final: 8 residues processed: 108 average time/residue: 0.4509 time to fit residues: 51.7226 Evaluate side-chains 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 271 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112373 restraints weight = 7349.333| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.21 r_work: 0.3055 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7575 Z= 0.127 Angle : 0.478 5.182 10167 Z= 0.256 Chirality : 0.039 0.125 1011 Planarity : 0.004 0.051 1242 Dihedral : 13.312 113.328 1269 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.14 % Allowed : 8.97 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.28), residues: 843 helix: 2.09 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 1.32 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 268 TYR 0.013 0.001 TYR A 271 PHE 0.013 0.002 PHE A 155 TRP 0.012 0.001 TRP C 19 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7572) covalent geometry : angle 0.47774 / 0.26 (10167) hydrogen bonds : bond 0.05476 / 3.67 ( 450) hydrogen bonds : angle 3.34409 / 2.40 ( 1323) Misc. bond : bond 0.00022 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.294 Fit side-chains REVERT: A 68 GLN cc_start: 0.8170 (mp10) cc_final: 0.7539 (mp10) REVERT: A 148 MET cc_start: 0.8436 (ttp) cc_final: 0.8121 (ttp) REVERT: A 221 MET cc_start: 0.7071 (tmm) cc_final: 0.6848 (tmm) REVERT: A 272 ASP cc_start: 0.7271 (p0) cc_final: 0.7033 (p0) REVERT: B 9 GLN cc_start: 0.8231 (tt0) cc_final: 0.7869 (tt0) REVERT: B 92 ASP cc_start: 0.8142 (m-30) cc_final: 0.7908 (m-30) REVERT: B 272 ASP cc_start: 0.7566 (p0) cc_final: 0.7222 (p0) outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 0.5017 time to fit residues: 53.6358 Evaluate side-chains 99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112332 restraints weight = 7215.123| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.15 r_work: 0.3210 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7575 Z= 0.146 Angle : 0.500 5.162 10167 Z= 0.268 Chirality : 0.040 0.124 1011 Planarity : 0.004 0.053 1242 Dihedral : 13.079 114.353 1269 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.57 % Allowed : 10.54 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.28), residues: 843 helix: 2.07 (0.21), residues: 600 sheet: None (None), residues: 0 loop : 1.24 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 164 TYR 0.016 0.002 TYR A 271 PHE 0.011 0.002 PHE C 173 TRP 0.013 0.002 TRP C 19 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 7572) covalent geometry : angle 0.50006 / 0.27 (10167) hydrogen bonds : bond 0.05936 / 3.99 ( 450) hydrogen bonds : angle 3.39051 / 2.43 ( 1323) Misc. bond : bond 0.00009 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.265 Fit side-chains REVERT: A 50 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: A 59 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7471 (mmtm) REVERT: A 68 GLN cc_start: 0.8223 (mp10) cc_final: 0.7794 (mp10) REVERT: A 148 MET cc_start: 0.8390 (ttp) cc_final: 0.8145 (ttp) REVERT: A 221 MET cc_start: 0.7135 (tmm) cc_final: 0.6888 (tmm) REVERT: A 272 ASP cc_start: 0.7378 (p0) cc_final: 0.7145 (p0) REVERT: B 9 GLN cc_start: 0.8252 (tt0) cc_final: 0.8014 (tt0) REVERT: B 92 ASP cc_start: 0.8113 (m-30) cc_final: 0.7878 (m-30) REVERT: B 272 ASP cc_start: 0.7666 (p0) cc_final: 0.7309 (p0) REVERT: C 92 ASP cc_start: 0.8068 (m-30) cc_final: 0.7805 (m-30) outliers start: 11 outliers final: 11 residues processed: 104 average time/residue: 0.5213 time to fit residues: 57.5212 Evaluate side-chains 107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 271 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111358 restraints weight = 7211.290| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.16 r_work: 0.3012 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7575 Z= 0.179 Angle : 0.542 5.245 10167 Z= 0.289 Chirality : 0.041 0.127 1011 Planarity : 0.005 0.054 1242 Dihedral : 13.602 114.896 1269 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.57 % Allowed : 11.97 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.28), residues: 843 helix: 1.97 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 1.10 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 268 TYR 0.021 0.002 TYR A 271 PHE 0.013 0.002 PHE C 219 TRP 0.015 0.002 TRP C 19 HIS 0.006 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 7572) covalent geometry : angle 0.54155 / 0.29 (10167) hydrogen bonds : bond 0.06528 / 4.38 ( 450) hydrogen bonds : angle 3.48780 / 2.50 ( 1323) Misc. bond : bond 0.00011 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.228 Fit side-chains REVERT: A 50 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: A 59 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7483 (mmtm) REVERT: A 68 GLN cc_start: 0.8195 (mp10) cc_final: 0.7587 (mp10) REVERT: A 148 MET cc_start: 0.8460 (ttp) cc_final: 0.8193 (ttp) REVERT: A 221 MET cc_start: 0.7136 (tmm) cc_final: 0.6893 (tmm) REVERT: A 272 ASP cc_start: 0.7370 (p0) cc_final: 0.7146 (p0) REVERT: B 9 GLN cc_start: 0.8333 (tt0) cc_final: 0.8049 (tt0) REVERT: B 272 ASP cc_start: 0.7684 (p0) cc_final: 0.7344 (p0) outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 0.4696 time to fit residues: 53.9521 Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 271 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN C 9 GLN C 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115448 restraints weight = 7174.554| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.16 r_work: 0.3058 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7575 Z= 0.117 Angle : 0.464 5.401 10167 Z= 0.249 Chirality : 0.038 0.125 1011 Planarity : 0.004 0.052 1242 Dihedral : 12.427 113.598 1269 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.99 % Allowed : 11.97 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.28), residues: 843 helix: 2.17 (0.21), residues: 603 sheet: None (None), residues: 0 loop : 1.23 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 268 TYR 0.012 0.001 TYR B 271 PHE 0.011 0.001 PHE B 173 TRP 0.012 0.001 TRP B 177 HIS 0.003 0.000 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7572) covalent geometry : angle 0.46432 / 0.25 (10167) hydrogen bonds : bond 0.05159 / 3.46 ( 450) hydrogen bonds : angle 3.25291 / 2.33 ( 1323) Misc. bond : bond 0.00024 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.310 Fit side-chains REVERT: A 59 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7448 (mmtm) REVERT: A 68 GLN cc_start: 0.8056 (mp10) cc_final: 0.7550 (mp10) REVERT: A 148 MET cc_start: 0.8493 (ttp) cc_final: 0.8241 (ttp) REVERT: A 272 ASP cc_start: 0.7314 (p0) cc_final: 0.7099 (p0) REVERT: B 9 GLN cc_start: 0.8284 (tt0) cc_final: 0.8006 (tt0) REVERT: B 272 ASP cc_start: 0.7577 (p0) cc_final: 0.7250 (p0) REVERT: C 191 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7780 (tttm) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.5129 time to fit residues: 58.3455 Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114343 restraints weight = 7257.552| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.17 r_work: 0.3041 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7575 Z= 0.128 Angle : 0.476 5.297 10167 Z= 0.255 Chirality : 0.039 0.125 1011 Planarity : 0.004 0.052 1242 Dihedral : 12.428 113.949 1269 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.57 % Allowed : 12.39 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.28), residues: 843 helix: 2.17 (0.21), residues: 603 sheet: None (None), residues: 0 loop : 1.22 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 268 TYR 0.013 0.001 TYR A 271 PHE 0.011 0.001 PHE A 173 TRP 0.012 0.001 TRP C 19 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7572) covalent geometry : angle 0.47630 / 0.26 (10167) hydrogen bonds : bond 0.05466 / 3.67 ( 450) hydrogen bonds : angle 3.27565 / 2.34 ( 1323) Misc. bond : bond 0.00014 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.258 Fit side-chains REVERT: A 59 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7440 (mmtm) REVERT: A 68 GLN cc_start: 0.8063 (mp10) cc_final: 0.7553 (mp10) REVERT: A 148 MET cc_start: 0.8440 (ttp) cc_final: 0.8190 (ttp) REVERT: B 9 GLN cc_start: 0.8287 (tt0) cc_final: 0.7968 (tt0) REVERT: B 122 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7903 (mtm) REVERT: B 272 ASP cc_start: 0.7631 (p0) cc_final: 0.7300 (p0) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 0.5196 time to fit residues: 57.8935 Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106986 restraints weight = 7264.972| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.17 r_work: 0.3118 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7575 Z= 0.217 Angle : 0.581 5.285 10167 Z= 0.309 Chirality : 0.043 0.129 1011 Planarity : 0.005 0.054 1242 Dihedral : 13.791 115.479 1269 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.14 % Allowed : 11.97 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.28), residues: 843 helix: 1.90 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 1.06 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 164 TYR 0.024 0.002 TYR A 271 PHE 0.014 0.002 PHE C 219 TRP 0.015 0.002 TRP B 52 HIS 0.006 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 ( 7572) covalent geometry : angle 0.58092 / 0.31 (10167) hydrogen bonds : bond 0.06991 / 4.69 ( 450) hydrogen bonds : angle 3.54815 / 2.54 ( 1323) Misc. bond : bond 0.00029 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.325 Fit side-chains REVERT: A 59 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7540 (mmtm) REVERT: A 148 MET cc_start: 0.8511 (ttp) cc_final: 0.8218 (ttp) REVERT: A 191 LYS cc_start: 0.8456 (tttm) cc_final: 0.8103 (tttm) REVERT: B 9 GLN cc_start: 0.8318 (tt0) cc_final: 0.8058 (tt0) REVERT: B 122 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8255 (mtm) REVERT: B 272 ASP cc_start: 0.7816 (p0) cc_final: 0.7482 (p0) REVERT: C 221 MET cc_start: 0.7372 (tmt) cc_final: 0.7087 (tmm) outliers start: 15 outliers final: 12 residues processed: 103 average time/residue: 0.4906 time to fit residues: 53.7813 Evaluate side-chains 106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 271 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113002 restraints weight = 7171.323| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.13 r_work: 0.3053 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7575 Z= 0.131 Angle : 0.489 5.339 10167 Z= 0.262 Chirality : 0.039 0.126 1011 Planarity : 0.004 0.053 1242 Dihedral : 12.742 114.145 1269 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.57 % Allowed : 12.68 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.28), residues: 843 helix: 2.08 (0.21), residues: 603 sheet: None (None), residues: 0 loop : 1.17 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 235 TYR 0.014 0.001 TYR A 271 PHE 0.011 0.001 PHE A 173 TRP 0.012 0.001 TRP C 19 HIS 0.004 0.000 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7572) covalent geometry : angle 0.48858 / 0.26 (10167) hydrogen bonds : bond 0.05507 / 3.70 ( 450) hydrogen bonds : angle 3.32234 / 2.37 ( 1323) Misc. bond : bond 0.00017 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.331 Fit side-chains REVERT: A 59 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7402 (mmtm) REVERT: A 148 MET cc_start: 0.8454 (ttp) cc_final: 0.8153 (ttp) REVERT: B 9 GLN cc_start: 0.8295 (tt0) cc_final: 0.8017 (tt0) REVERT: B 122 MET cc_start: 0.8265 (mtm) cc_final: 0.7990 (mtm) REVERT: B 272 ASP cc_start: 0.7588 (p0) cc_final: 0.7282 (p0) outliers start: 11 outliers final: 11 residues processed: 104 average time/residue: 0.4715 time to fit residues: 52.0623 Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN C 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110309 restraints weight = 7179.354| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.19 r_work: 0.3020 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7575 Z= 0.153 Angle : 0.513 5.231 10167 Z= 0.274 Chirality : 0.040 0.127 1011 Planarity : 0.005 0.053 1242 Dihedral : 12.962 114.548 1269 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.99 % Allowed : 12.25 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.28), residues: 843 helix: 2.11 (0.21), residues: 597 sheet: None (None), residues: 0 loop : 1.09 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 164 TYR 0.017 0.002 TYR A 271 PHE 0.012 0.002 PHE C 219 TRP 0.014 0.002 TRP C 19 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 7572) covalent geometry : angle 0.51274 / 0.27 (10167) hydrogen bonds : bond 0.05967 / 4.01 ( 450) hydrogen bonds : angle 3.38228 / 2.42 ( 1323) Misc. bond : bond 0.00006 / 0.00 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.94 seconds wall clock time: 36 minutes 15.11 seconds (2175.11 seconds total)