Starting phenix.real_space_refine on Fri Aug 22 23:07:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqc_16795/08_2025/8cqc_16795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqc_16795/08_2025/8cqc_16795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cqc_16795/08_2025/8cqc_16795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqc_16795/08_2025/8cqc_16795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cqc_16795/08_2025/8cqc_16795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqc_16795/08_2025/8cqc_16795.map" } resolution = 2.82 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= 0.019 sd= 0.276 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5880 2.51 5 N 1300 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8735 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "B" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "C" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "D" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "E" Number of atoms: 1721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 bond proxies already assigned to first conformer: 1757 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.95, per 1000 atoms: 0.45 Number of scatterers: 8735 At special positions: 0 Unit cell: (102.479, 101.475, 67.3149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1500 8.00 N 1300 7.00 C 5880 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 532.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 90.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 30 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 56 through 87 removed outlier: 4.605A pdb=" N THR A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 118 removed outlier: 3.516A pdb=" N TRP A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 4.245A pdb=" N PHE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 144 Processing helix chain 'A' and resid 148 through 169 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 220 through 249 removed outlier: 4.169A pdb=" N PHE A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 56 through 87 removed outlier: 4.603A pdb=" N THR B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N SER B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 118 removed outlier: 3.509A pdb=" N TRP B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 4.262A pdb=" N PHE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 Processing helix chain 'B' and resid 148 through 169 Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 220 through 249 removed outlier: 4.166A pdb=" N PHE B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 51 Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 56 through 87 removed outlier: 4.604A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 118 removed outlier: 3.511A pdb=" N TRP C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 4.242A pdb=" N PHE C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 144 Processing helix chain 'C' and resid 148 through 169 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 220 through 249 removed outlier: 4.156A pdb=" N PHE C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 51 Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 56 through 87 removed outlier: 4.602A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 118 removed outlier: 3.510A pdb=" N TRP D 99 " --> pdb=" O ARG D 95 " (cutoff:3.500A) Proline residue: D 104 - end of helix removed outlier: 4.229A pdb=" N PHE D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 144 Processing helix chain 'D' and resid 148 through 169 Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 180 through 197 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 220 through 249 removed outlier: 4.160A pdb=" N PHE D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 51 Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 56 through 87 removed outlier: 4.603A pdb=" N THR E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 118 removed outlier: 3.511A pdb=" N TRP E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Proline residue: E 104 - end of helix removed outlier: 4.278A pdb=" N PHE E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 144 Processing helix chain 'E' and resid 148 through 169 Processing helix chain 'E' and resid 170 through 177 Processing helix chain 'E' and resid 180 through 197 Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 220 through 249 removed outlier: 4.137A pdb=" N PHE E 235 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) 740 hydrogen bonds defined for protein. 2215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1270 1.29 - 1.42: 2685 1.42 - 1.55: 4910 1.55 - 1.68: 15 1.68 - 1.81: 95 Bond restraints: 8975 Sorted by residual: bond pdb=" C ARG A 95 " pdb=" O ARG A 95 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.31e-02 5.83e+03 3.27e+01 bond pdb=" C ARG B 95 " pdb=" O ARG B 95 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.31e-02 5.83e+03 3.27e+01 bond pdb=" C ARG C 95 " pdb=" O ARG C 95 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.31e-02 5.83e+03 3.26e+01 bond pdb=" C ARG E 95 " pdb=" O ARG E 95 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.31e-02 5.83e+03 3.26e+01 bond pdb=" C ARG D 95 " pdb=" O ARG D 95 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.31e-02 5.83e+03 3.22e+01 ... (remaining 8970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 11514 1.33 - 2.66: 544 2.66 - 3.99: 151 3.99 - 5.32: 46 5.32 - 6.65: 10 Bond angle restraints: 12265 Sorted by residual: angle pdb=" N ARG E 95 " pdb=" CA ARG E 95 " pdb=" C ARG E 95 " ideal model delta sigma weight residual 113.18 106.53 6.65 1.21e+00 6.83e-01 3.02e+01 angle pdb=" N ARG C 95 " pdb=" CA ARG C 95 " pdb=" C ARG C 95 " ideal model delta sigma weight residual 113.18 106.56 6.62 1.21e+00 6.83e-01 2.99e+01 angle pdb=" N ARG D 95 " pdb=" CA ARG D 95 " pdb=" C ARG D 95 " ideal model delta sigma weight residual 113.18 106.57 6.61 1.21e+00 6.83e-01 2.99e+01 angle pdb=" N ARG A 95 " pdb=" CA ARG A 95 " pdb=" C ARG A 95 " ideal model delta sigma weight residual 113.18 106.58 6.60 1.21e+00 6.83e-01 2.98e+01 angle pdb=" N ARG B 95 " pdb=" CA ARG B 95 " pdb=" C ARG B 95 " ideal model delta sigma weight residual 113.18 106.60 6.58 1.21e+00 6.83e-01 2.96e+01 ... (remaining 12260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4694 17.18 - 34.36: 241 34.36 - 51.53: 35 51.53 - 68.71: 0 68.71 - 85.89: 10 Dihedral angle restraints: 4980 sinusoidal: 1815 harmonic: 3165 Sorted by residual: dihedral pdb=" CB GLU D 246 " pdb=" CG GLU D 246 " pdb=" CD GLU D 246 " pdb=" OE1 GLU D 246 " ideal model delta sinusoidal sigma weight residual 0.00 85.89 -85.89 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CB GLU B 246 " pdb=" CG GLU B 246 " pdb=" CD GLU B 246 " pdb=" OE1 GLU B 246 " ideal model delta sinusoidal sigma weight residual 0.00 84.31 -84.31 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" CB GLU A 246 " pdb=" CG GLU A 246 " pdb=" CD GLU A 246 " pdb=" OE1 GLU A 246 " ideal model delta sinusoidal sigma weight residual 0.00 83.42 -83.42 1 3.00e+01 1.11e-03 9.44e+00 ... (remaining 4977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 806 0.027 - 0.053: 355 0.053 - 0.080: 127 0.080 - 0.107: 60 0.107 - 0.133: 27 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA ILE D 72 " pdb=" N ILE D 72 " pdb=" C ILE D 72 " pdb=" CB ILE D 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 72 " pdb=" N ILE B 72 " pdb=" C ILE B 72 " pdb=" CB ILE B 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE C 72 " pdb=" N ILE C 72 " pdb=" C ILE C 72 " pdb=" CB ILE C 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1372 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 75 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C TRP C 75 " 0.049 2.00e-02 2.50e+03 pdb=" O TRP C 75 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS C 76 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 75 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C TRP D 75 " -0.049 2.00e-02 2.50e+03 pdb=" O TRP D 75 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS D 76 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 75 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C TRP A 75 " -0.049 2.00e-02 2.50e+03 pdb=" O TRP A 75 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 76 " 0.016 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3783 2.91 - 3.40: 9706 3.40 - 3.90: 15388 3.90 - 4.40: 17813 4.40 - 4.90: 29433 Nonbonded interactions: 76123 Sorted by model distance: nonbonded pdb=" O LYS E 58 " pdb=" O HOH E 401 " model vdw 2.406 3.040 nonbonded pdb=" O LYS B 58 " pdb=" O HOH B 401 " model vdw 2.408 3.040 nonbonded pdb=" O LYS A 58 " pdb=" O HOH A 401 " model vdw 2.408 3.040 nonbonded pdb=" O LYS C 58 " pdb=" O HOH C 401 " model vdw 2.408 3.040 nonbonded pdb=" O LYS D 58 " pdb=" O HOH D 401 " model vdw 2.408 3.040 ... (remaining 76118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.50 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: 0.570 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 12.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.006 0.075 8980 Z= 0.431 Angle : 0.718 6.653 12265 Z= 0.476 Chirality : 0.039 0.133 1375 Planarity : 0.004 0.034 1460 Dihedral : 10.914 85.888 2970 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.34 % Allowed : 3.48 % Favored : 96.18 % 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 aren not related in a simple way. whole: 0.69 (0.25), residues: 1070 helix: 0.73 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.13 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 52 TYR 0.015 0.002 TYR B 205 PHE 0.014 0.002 PHE A 235 TRP 0.011 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00623 ( 8975) covalent geometry : angle 0.71779 (12265) hydrogen bonds : bond 0.11886 ( 740) hydrogen bonds : angle 5.90480 ( 2215) Misc. bond : bond 0.03886 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7778 (mtmm) REVERT: A 192 TYR cc_start: 0.7804 (m-80) cc_final: 0.7520 (m-80) REVERT: B 192 TYR cc_start: 0.7882 (m-80) cc_final: 0.7304 (m-80) REVERT: C 53 ASP cc_start: 0.7751 (m-30) cc_final: 0.7447 (m-30) REVERT: C 190 MET cc_start: 0.8570 (mtp) cc_final: 0.8312 (mtm) REVERT: C 192 TYR cc_start: 0.7854 (m-80) cc_final: 0.7199 (m-80) REVERT: E 58 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7883 (mtmm) REVERT: E 192 TYR cc_start: 0.7981 (m-80) cc_final: 0.7368 (m-80) outliers start: 3 outliers final: 3 residues processed: 115 average time/residue: 0.4458 time to fit residues: 55.2561 Evaluate side-chains 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN B 184 GLN C 184 GLN D 184 GLN D 231 ASN E 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124592 restraints weight = 28060.777| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 6.89 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8980 Z= 0.140 Angle : 0.505 8.027 12265 Z= 0.276 Chirality : 0.038 0.129 1375 Planarity : 0.004 0.032 1460 Dihedral : 4.187 40.122 1231 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.90 % Allowed : 8.43 % Favored : 90.67 % 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 aren not related in a simple way. whole: 2.20 (0.25), residues: 1070 helix: 1.78 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.15 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 54 TYR 0.019 0.001 TYR E 77 PHE 0.014 0.001 PHE D 235 TRP 0.016 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8975) covalent geometry : angle 0.50457 (12265) hydrogen bonds : bond 0.04907 ( 740) hydrogen bonds : angle 3.95428 ( 2215) Misc. bond : bond 0.00063 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7488 (t80) cc_final: 0.7280 (t80) REVERT: A 166 GLU cc_start: 0.7092 (tp30) cc_final: 0.6732 (mm-30) REVERT: A 192 TYR cc_start: 0.7893 (m-80) cc_final: 0.7662 (m-80) REVERT: B 192 TYR cc_start: 0.8030 (m-80) cc_final: 0.7520 (m-80) REVERT: C 53 ASP cc_start: 0.7296 (m-30) cc_final: 0.7008 (m-30) REVERT: C 190 MET cc_start: 0.8563 (mtp) cc_final: 0.8308 (mtm) REVERT: C 192 TYR cc_start: 0.7976 (m-80) cc_final: 0.7382 (m-80) REVERT: E 58 LYS cc_start: 0.7692 (mtmt) cc_final: 0.7484 (mtmm) REVERT: E 192 TYR cc_start: 0.8042 (m-80) cc_final: 0.7517 (m-80) outliers start: 8 outliers final: 4 residues processed: 121 average time/residue: 0.4560 time to fit residues: 59.8461 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN B 184 GLN C 184 GLN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN ** E 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.165428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126537 restraints weight = 22168.120| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 5.28 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8980 Z= 0.144 Angle : 0.526 12.428 12265 Z= 0.278 Chirality : 0.038 0.111 1375 Planarity : 0.004 0.034 1460 Dihedral : 3.966 41.749 1227 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.12 % Allowed : 8.99 % Favored : 89.89 % 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 aren not related in a simple way. whole: 2.34 (0.25), residues: 1070 helix: 1.86 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.95 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 52 TYR 0.011 0.001 TYR B 79 PHE 0.013 0.002 PHE E 235 TRP 0.017 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8975) covalent geometry : angle 0.52568 (12265) hydrogen bonds : bond 0.05041 ( 740) hydrogen bonds : angle 3.80604 ( 2215) Misc. bond : bond 0.00089 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7855 (m-80) cc_final: 0.7573 (m-80) REVERT: B 192 TYR cc_start: 0.8053 (m-80) cc_final: 0.7565 (m-80) REVERT: C 190 MET cc_start: 0.8599 (mtp) cc_final: 0.8376 (mtm) REVERT: C 192 TYR cc_start: 0.7954 (m-80) cc_final: 0.7366 (m-80) REVERT: D 147 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6902 (tpp) REVERT: E 58 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7681 (mtmm) REVERT: E 192 TYR cc_start: 0.8058 (m-80) cc_final: 0.7521 (m-80) outliers start: 10 outliers final: 5 residues processed: 113 average time/residue: 0.4802 time to fit residues: 58.5841 Evaluate side-chains 103 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 231 ASN ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 231 ASN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN ** E 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.163522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120928 restraints weight = 25730.872| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 6.38 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8980 Z= 0.168 Angle : 0.539 10.729 12265 Z= 0.287 Chirality : 0.039 0.116 1375 Planarity : 0.004 0.035 1460 Dihedral : 4.110 39.995 1227 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.24 % Allowed : 9.55 % Favored : 89.21 % 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 aren not related in a simple way. whole: 2.23 (0.25), residues: 1070 helix: 1.79 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.00 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 52 TYR 0.011 0.001 TYR B 79 PHE 0.014 0.002 PHE D 235 TRP 0.016 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8975) covalent geometry : angle 0.53880 (12265) hydrogen bonds : bond 0.05435 ( 740) hydrogen bonds : angle 3.90908 ( 2215) Misc. bond : bond 0.00125 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7978 (m-80) cc_final: 0.7760 (m-80) REVERT: B 192 TYR cc_start: 0.8028 (m-80) cc_final: 0.7524 (m-80) REVERT: C 192 TYR cc_start: 0.7980 (m-80) cc_final: 0.7429 (m-80) REVERT: E 192 TYR cc_start: 0.8079 (m-80) cc_final: 0.7566 (m-80) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.5281 time to fit residues: 60.2628 Evaluate side-chains 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** C 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.168124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129100 restraints weight = 23560.896| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 5.10 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8980 Z= 0.128 Angle : 0.486 9.469 12265 Z= 0.258 Chirality : 0.037 0.108 1375 Planarity : 0.003 0.033 1460 Dihedral : 3.898 38.473 1227 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.24 % Allowed : 9.89 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.25), residues: 1070 helix: 1.92 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -0.99 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.008 0.001 TYR D 187 PHE 0.012 0.001 PHE D 235 TRP 0.020 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8975) covalent geometry : angle 0.48568 (12265) hydrogen bonds : bond 0.04703 ( 740) hydrogen bonds : angle 3.72095 ( 2215) Misc. bond : bond 0.00079 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7885 (m-80) cc_final: 0.7556 (m-80) REVERT: B 192 TYR cc_start: 0.8024 (m-80) cc_final: 0.7562 (m-80) REVERT: C 192 TYR cc_start: 0.7901 (m-80) cc_final: 0.7338 (m-80) REVERT: E 192 TYR cc_start: 0.8084 (m-80) cc_final: 0.7605 (m-80) outliers start: 9 outliers final: 5 residues processed: 106 average time/residue: 0.4377 time to fit residues: 50.0773 Evaluate side-chains 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN C 231 ASN D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.095089 restraints weight = 16861.042| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.57 r_work: 0.2727 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8980 Z= 0.207 Angle : 0.590 11.369 12265 Z= 0.314 Chirality : 0.041 0.145 1375 Planarity : 0.004 0.036 1460 Dihedral : 4.245 38.377 1227 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.80 % Allowed : 10.22 % Favored : 87.98 % 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 aren not related in a simple way. whole: 2.06 (0.25), residues: 1070 helix: 1.63 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.72 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.017 0.002 TYR D 79 PHE 0.016 0.002 PHE A 235 TRP 0.019 0.002 TRP D 84 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 8975) covalent geometry : angle 0.58985 (12265) hydrogen bonds : bond 0.05893 ( 740) hydrogen bonds : angle 4.02755 ( 2215) Misc. bond : bond 0.00162 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 192 TYR cc_start: 0.8289 (m-80) cc_final: 0.8081 (m-80) REVERT: B 192 TYR cc_start: 0.8342 (m-80) cc_final: 0.7746 (m-80) REVERT: C 58 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8096 (mtmm) REVERT: C 128 LEU cc_start: 0.7315 (mt) cc_final: 0.7112 (mt) REVERT: C 192 TYR cc_start: 0.8282 (m-80) cc_final: 0.7615 (m-80) REVERT: D 147 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6502 (tpp) REVERT: E 192 TYR cc_start: 0.8491 (m-80) cc_final: 0.7832 (m-80) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.4439 time to fit residues: 51.6390 Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN B 184 GLN ** C 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.163357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124471 restraints weight = 20197.451| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.99 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8980 Z= 0.157 Angle : 0.549 12.342 12265 Z= 0.288 Chirality : 0.039 0.113 1375 Planarity : 0.004 0.034 1460 Dihedral : 4.110 38.138 1227 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.35 % Allowed : 10.56 % Favored : 88.09 % 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 aren not related in a simple way. whole: 2.11 (0.24), residues: 1070 helix: 1.67 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.78 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 95 TYR 0.010 0.001 TYR D 79 PHE 0.013 0.002 PHE E 235 TRP 0.020 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8975) covalent geometry : angle 0.54904 (12265) hydrogen bonds : bond 0.05216 ( 740) hydrogen bonds : angle 3.90537 ( 2215) Misc. bond : bond 0.00111 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7955 (m-80) cc_final: 0.7692 (m-80) REVERT: B 192 TYR cc_start: 0.8066 (m-80) cc_final: 0.7605 (m-80) REVERT: C 192 TYR cc_start: 0.7911 (m-80) cc_final: 0.7430 (m-80) REVERT: D 147 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6850 (tpp) REVERT: E 192 TYR cc_start: 0.8123 (m-80) cc_final: 0.7629 (m-80) outliers start: 11 outliers final: 8 residues processed: 105 average time/residue: 0.4917 time to fit residues: 55.5367 Evaluate side-chains 107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN C 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.162719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096483 restraints weight = 17773.259| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.05 r_work: 0.2753 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8980 Z= 0.173 Angle : 0.533 5.217 12265 Z= 0.287 Chirality : 0.039 0.118 1375 Planarity : 0.004 0.035 1460 Dihedral : 4.165 37.892 1227 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.80 % Allowed : 10.56 % Favored : 87.64 % 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 aren not related in a simple way. whole: 2.07 (0.24), residues: 1070 helix: 1.64 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.80 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.011 0.002 TYR D 187 PHE 0.014 0.002 PHE A 235 TRP 0.017 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8975) covalent geometry : angle 0.53339 (12265) hydrogen bonds : bond 0.05446 ( 740) hydrogen bonds : angle 3.96408 ( 2215) Misc. bond : bond 0.00126 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.8141 (m-80) cc_final: 0.7873 (m-80) REVERT: B 192 TYR cc_start: 0.8204 (m-80) cc_final: 0.7594 (m-80) REVERT: C 192 TYR cc_start: 0.8193 (m-80) cc_final: 0.7587 (m-80) REVERT: D 80 MET cc_start: 0.6818 (tpp) cc_final: 0.6073 (mmp) REVERT: D 147 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6466 (tpp) REVERT: E 192 TYR cc_start: 0.8430 (m-80) cc_final: 0.7760 (m-80) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.4797 time to fit residues: 54.8159 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 81 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN B 184 GLN D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.163665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124686 restraints weight = 24300.125| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 5.26 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8980 Z= 0.155 Angle : 0.514 5.325 12265 Z= 0.276 Chirality : 0.039 0.114 1375 Planarity : 0.004 0.034 1460 Dihedral : 4.097 37.573 1227 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.57 % Allowed : 10.67 % Favored : 87.75 % 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 aren not related in a simple way. whole: 2.19 (0.24), residues: 1070 helix: 1.73 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.81 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.011 0.001 TYR C 79 PHE 0.013 0.002 PHE D 235 TRP 0.019 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8975) covalent geometry : angle 0.51420 (12265) hydrogen bonds : bond 0.05154 ( 740) hydrogen bonds : angle 3.89717 ( 2215) Misc. bond : bond 0.00112 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.7957 (m-80) cc_final: 0.7630 (m-80) REVERT: B 192 TYR cc_start: 0.8047 (m-80) cc_final: 0.7599 (m-80) REVERT: C 192 TYR cc_start: 0.7929 (m-80) cc_final: 0.7440 (m-80) REVERT: D 80 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6131 (mmp) REVERT: D 147 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6887 (tpp) REVERT: E 192 TYR cc_start: 0.8099 (m-80) cc_final: 0.7605 (m-80) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.4541 time to fit residues: 51.3327 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN D 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.165238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101990 restraints weight = 14924.999| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.84 r_work: 0.2822 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8980 Z= 0.141 Angle : 0.496 5.353 12265 Z= 0.267 Chirality : 0.038 0.111 1375 Planarity : 0.004 0.034 1460 Dihedral : 4.015 37.278 1227 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 10.90 % Favored : 87.75 % 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 aren not related in a simple way. whole: 2.29 (0.24), residues: 1070 helix: 1.85 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.18 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.010 0.001 TYR C 79 PHE 0.013 0.002 PHE D 235 TRP 0.018 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8975) covalent geometry : angle 0.49596 (12265) hydrogen bonds : bond 0.04890 ( 740) hydrogen bonds : angle 3.81492 ( 2215) Misc. bond : bond 0.00098 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 TYR cc_start: 0.8113 (m-80) cc_final: 0.7781 (m-80) REVERT: B 192 TYR cc_start: 0.8199 (m-80) cc_final: 0.7651 (m-80) REVERT: C 192 TYR cc_start: 0.8156 (m-80) cc_final: 0.7571 (m-80) REVERT: D 80 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.5960 (mmp) REVERT: D 147 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6518 (tpp) REVERT: E 192 TYR cc_start: 0.8361 (m-80) cc_final: 0.7727 (m-80) outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.5143 time to fit residues: 58.2501 Evaluate side-chains 107 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 30 optimal weight: 0.0980 chunk 34 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN D 184 GLN ** E 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.164362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125086 restraints weight = 21614.078| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 4.94 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8980 Z= 0.154 Angle : 0.516 5.479 12265 Z= 0.277 Chirality : 0.038 0.114 1375 Planarity : 0.004 0.034 1460 Dihedral : 4.067 37.317 1227 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.57 % Allowed : 10.79 % Favored : 87.64 % 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 aren not related in a simple way. whole: 2.25 (0.24), residues: 1070 helix: 1.82 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.17 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.010 0.001 TYR D 187 PHE 0.013 0.002 PHE D 235 TRP 0.018 0.001 TRP D 75 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8975) covalent geometry : angle 0.51573 (12265) hydrogen bonds : bond 0.05131 ( 740) hydrogen bonds : angle 3.87400 ( 2215) Misc. bond : bond 0.00112 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.67 seconds wall clock time: 43 minutes 41.65 seconds (2621.65 seconds total)