Starting phenix.real_space_refine on Thu Mar 13 01:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqc_16795/03_2025/8cqc_16795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqc_16795/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cqc_16795/03_2025/8cqc_16795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqc_16795/03_2025/8cqc_16795.map" model { file = "/net/cci-nas-00/data/ceres_data/8cqc_16795/03_2025/8cqc_16795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqc_16795/03_2025/8cqc_16795.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 11.44, per 1000 atoms: 1.31 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: 2.73 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 0.85 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: 2.67 Time building geometry restraints manager: 3.14 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 32.090 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.400 ------------------------------------------------------------------------------- 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 8975 Z= 0.379 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (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 TRP 0.011 0.001 TRP D 75 PHE 0.014 0.002 PHE A 235 TYR 0.015 0.002 TYR B 205 ARG 0.003 0.001 ARG E 52 *********************** 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 : 0.848 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: 0.8328 (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: 1.0085 time to fit residues: 125.1762 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 : 0.822 ------------------------------------------------------------------------------- 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 88 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 184 GLN D 184 GLN D 231 ASN ** E 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.166514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127908 restraints weight = 20266.261| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 5.05 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8975 Z= 0.199 Angle : 0.513 8.872 12265 Z= 0.280 Chirality : 0.038 0.126 1375 Planarity : 0.004 0.033 1460 Dihedral : 4.205 40.530 1231 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.90 % Allowed : 8.54 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1070 helix: 1.76 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.16 (0.55), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 75 PHE 0.014 0.002 PHE D 235 TYR 0.020 0.001 TYR E 77 ARG 0.003 0.001 ARG B 54 *********************** 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 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7402 (tp30) cc_final: 0.7033 (mm-30) REVERT: A 192 TYR cc_start: 0.7971 (m-80) cc_final: 0.7745 (m-80) REVERT: B 192 TYR cc_start: 0.8101 (m-80) cc_final: 0.7587 (m-80) REVERT: C 190 MET cc_start: 0.8607 (mtp) cc_final: 0.8338 (mtm) REVERT: C 192 TYR cc_start: 0.8001 (m-80) cc_final: 0.7419 (m-80) REVERT: E 58 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7734 (mtmm) REVERT: E 192 TYR cc_start: 0.8092 (m-80) cc_final: 0.7565 (m-80) outliers start: 8 outliers final: 4 residues processed: 115 average time/residue: 1.0438 time to fit residues: 130.0509 Evaluate side-chains 105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 59 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 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 = 0.3796 r_free = 0.3796 target = 0.162446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123018 restraints weight = 22071.226| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 5.11 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8975 Z= 0.294 Angle : 0.591 12.366 12265 Z= 0.313 Chirality : 0.041 0.119 1375 Planarity : 0.004 0.037 1460 Dihedral : 4.262 42.390 1227 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.69 % Allowed : 8.20 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.25), residues: 1070 helix: 1.65 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.03 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 75 PHE 0.016 0.002 PHE A 235 TYR 0.011 0.002 TYR A 187 ARG 0.003 0.001 ARG A 52 *********************** 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 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 TYR cc_start: 0.8066 (m-80) cc_final: 0.7547 (m-80) REVERT: C 58 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8064 (mtmm) REVERT: C 190 MET cc_start: 0.8673 (mtp) cc_final: 0.8428 (mtm) REVERT: C 192 TYR cc_start: 0.7949 (m-80) cc_final: 0.7377 (m-80) REVERT: D 147 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6929 (tpp) REVERT: E 58 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7807 (mtmm) REVERT: E 192 TYR cc_start: 0.8106 (m-80) cc_final: 0.7592 (m-80) outliers start: 15 outliers final: 8 residues processed: 110 average time/residue: 1.1224 time to fit residues: 133.2117 Evaluate side-chains 103 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain C 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 70 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 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 = 0.3826 r_free = 0.3826 target = 0.164762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125664 restraints weight = 23444.302| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 5.33 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8975 Z= 0.207 Angle : 0.524 8.702 12265 Z= 0.279 Chirality : 0.038 0.124 1375 Planarity : 0.004 0.034 1460 Dihedral : 4.052 40.900 1227 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.24 % Allowed : 9.66 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.25), residues: 1070 helix: 1.74 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.03 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 75 PHE 0.013 0.002 PHE D 235 TYR 0.009 0.001 TYR C 79 ARG 0.003 0.000 ARG E 95 *********************** 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 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 TYR cc_start: 0.8062 (m-80) cc_final: 0.7563 (m-80) REVERT: C 190 MET cc_start: 0.8620 (mtp) cc_final: 0.8404 (mtm) REVERT: C 192 TYR cc_start: 0.7982 (m-80) cc_final: 0.7448 (m-80) REVERT: E 192 TYR cc_start: 0.8095 (m-80) cc_final: 0.7599 (m-80) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 1.3149 time to fit residues: 151.2298 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 107 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 B 231 ASN ** C 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN C 231 ASN ** D 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN 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 = 0.163409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123763 restraints weight = 21689.079| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 5.02 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8975 Z= 0.245 Angle : 0.541 11.842 12265 Z= 0.287 Chirality : 0.039 0.115 1375 Planarity : 0.004 0.035 1460 Dihedral : 4.135 39.499 1227 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.57 % Allowed : 9.66 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.25), residues: 1070 helix: 1.71 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.06 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 75 PHE 0.014 0.002 PHE A 235 TYR 0.011 0.001 TYR D 187 ARG 0.002 0.000 ARG A 52 *********************** 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 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 TYR cc_start: 0.8074 (m-80) cc_final: 0.7577 (m-80) REVERT: C 192 TYR cc_start: 0.7952 (m-80) cc_final: 0.7426 (m-80) REVERT: D 147 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6972 (ttt) REVERT: E 192 TYR cc_start: 0.8102 (m-80) cc_final: 0.7579 (m-80) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 1.2183 time to fit residues: 139.9395 Evaluate side-chains 106 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE 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 163 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 Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 14 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 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 = 0.3847 r_free = 0.3847 target = 0.166597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127658 restraints weight = 22203.039| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 5.24 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8975 Z= 0.160 Angle : 0.472 4.916 12265 Z= 0.254 Chirality : 0.037 0.106 1375 Planarity : 0.003 0.033 1460 Dihedral : 3.900 37.966 1227 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.12 % Allowed : 10.56 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.25), residues: 1070 helix: 1.88 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.07 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 75 PHE 0.012 0.001 PHE D 235 TYR 0.008 0.001 TYR B 79 ARG 0.001 0.000 ARG A 52 *********************** 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 103 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 TYR cc_start: 0.7990 (m-80) cc_final: 0.7558 (m-80) REVERT: C 192 TYR cc_start: 0.7870 (m-80) cc_final: 0.7352 (m-80) REVERT: E 192 TYR cc_start: 0.8056 (m-80) cc_final: 0.7566 (m-80) outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 1.1572 time to fit residues: 124.1158 Evaluate side-chains 97 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102694 restraints weight = 18765.466| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.10 r_work: 0.2825 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 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 = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8975 Z= 0.155 Angle : 0.485 9.099 12265 Z= 0.259 Chirality : 0.037 0.107 1375 Planarity : 0.003 0.033 1460 Dihedral : 3.856 36.604 1227 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.24), residues: 1070 helix: 1.97 (0.16), residues: 955 sheet: None (None), residues: 0 loop : -1.07 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 75 PHE 0.013 0.001 PHE E 235 TYR 0.018 0.001 TYR D 77 ARG 0.002 0.000 ARG D 81 *********************** 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 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 TYR cc_start: 0.8041 (m-80) cc_final: 0.7486 (m-80) REVERT: C 192 TYR cc_start: 0.8019 (m-80) cc_final: 0.7402 (m-80) REVERT: E 192 TYR cc_start: 0.8283 (m-80) cc_final: 0.7642 (m-80) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 1.2035 time to fit residues: 129.5448 Evaluate side-chains 98 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 185 SER Chi-restraints excluded: chain D residue 107 ILE 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 78 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN C 184 GLN D 76 HIS B 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 = 0.3834 r_free = 0.3834 target = 0.165190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123736 restraints weight = 23061.385| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 5.85 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8975 Z= 0.204 Angle : 0.505 7.452 12265 Z= 0.269 Chirality : 0.038 0.111 1375 Planarity : 0.004 0.034 1460 Dihedral : 3.978 37.176 1227 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.80 % Allowed : 10.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.24), residues: 1070 helix: 1.86 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.76 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 75 PHE 0.014 0.002 PHE A 235 TYR 0.009 0.001 TYR D 187 ARG 0.002 0.000 ARG A 52 *********************** 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 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 TYR cc_start: 0.7976 (m-80) cc_final: 0.7541 (m-80) REVERT: C 192 TYR cc_start: 0.7903 (m-80) cc_final: 0.7385 (m-80) REVERT: D 147 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6933 (ttt) REVERT: E 192 TYR cc_start: 0.8074 (m-80) cc_final: 0.7600 (m-80) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 1.0896 time to fit residues: 129.2342 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 50 VAL 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 Chi-restraints excluded: chain E residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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 = 0.3861 r_free = 0.3861 target = 0.167595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.124078 restraints weight = 25265.415| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 6.51 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8975 Z= 0.162 Angle : 0.470 5.364 12265 Z= 0.252 Chirality : 0.037 0.107 1375 Planarity : 0.003 0.033 1460 Dihedral : 3.885 36.595 1227 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.35 % Allowed : 10.79 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.24), residues: 1070 helix: 1.96 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.75 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 75 PHE 0.012 0.001 PHE D 235 TYR 0.008 0.001 TYR E 79 ARG 0.001 0.000 ARG A 52 *********************** 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 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 TYR cc_start: 0.7909 (m-80) cc_final: 0.7472 (m-80) REVERT: C 192 TYR cc_start: 0.7874 (m-80) cc_final: 0.7374 (m-80) REVERT: D 147 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6830 (ttt) REVERT: E 192 TYR cc_start: 0.8046 (m-80) cc_final: 0.7610 (m-80) outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 1.0703 time to fit residues: 115.6077 Evaluate side-chains 99 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 88 optimal weight: 0.0670 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 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 = 0.3892 r_free = 0.3892 target = 0.169838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107154 restraints weight = 17875.728| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.12 r_work: 0.2830 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8975 Z= 0.158 Angle : 0.470 5.370 12265 Z= 0.251 Chirality : 0.036 0.106 1375 Planarity : 0.003 0.033 1460 Dihedral : 3.844 36.602 1227 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.01 % Allowed : 11.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.24), residues: 1070 helix: 2.01 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.71 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 75 PHE 0.012 0.001 PHE D 235 TYR 0.012 0.001 TYR E 79 ARG 0.001 0.000 ARG A 95 ********************** 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 100 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: B 192 TYR cc_start: 0.8030 (m-80) cc_final: 0.7493 (m-80) REVERT: C 192 TYR cc_start: 0.8038 (m-80) cc_final: 0.7452 (m-80) REVERT: D 147 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6672 (ttt) REVERT: E 192 TYR cc_start: 0.8280 (m-80) cc_final: 0.7642 (m-80) outliers start: 6 outliers final: 5 residues processed: 99 average time/residue: 1.0813 time to fit residues: 115.4288 Evaluate side-chains 100 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 102 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.167568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103777 restraints weight = 17624.408| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.91 r_work: 0.2833 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8975 Z= 0.165 Angle : 0.481 5.944 12265 Z= 0.256 Chirality : 0.037 0.106 1375 Planarity : 0.003 0.033 1460 Dihedral : 3.857 36.331 1227 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.24 % Allowed : 10.90 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.24), residues: 1070 helix: 2.02 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.73 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 75 PHE 0.013 0.001 PHE D 235 TYR 0.018 0.001 TYR E 79 ARG 0.002 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5430.08 seconds wall clock time: 96 minutes 38.75 seconds (5798.75 seconds total)