Starting phenix.real_space_refine on Wed Feb 4 11:42:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9inz_60713/02_2026/9inz_60713.cif Found real_map, /net/cci-nas-00/data/ceres_data/9inz_60713/02_2026/9inz_60713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9inz_60713/02_2026/9inz_60713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9inz_60713/02_2026/9inz_60713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9inz_60713/02_2026/9inz_60713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9inz_60713/02_2026/9inz_60713.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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 48 5.16 5 C 6948 2.51 5 N 1560 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10224 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'C14': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'C14': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'C14': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'C14': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'C14': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {'C14': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.37, per 1000 atoms: 0.23 Number of scatterers: 10224 At special positions: 0 Unit cell: (110.968, 106.392, 99.528, 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 48 16.00 O 1668 8.00 N 1560 7.00 C 6948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 447.5 milliseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 77.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 removed outlier: 3.969A pdb=" N GLN A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 40 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.686A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 111 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 150 through 177 removed outlier: 4.156A pdb=" N THR A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 238 removed outlier: 3.604A pdb=" N PHE A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 removed outlier: 3.983A pdb=" N GLN B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.613A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 111 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 150 through 177 removed outlier: 4.143A pdb=" N THR B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 238 removed outlier: 3.644A pdb=" N PHE B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 15 removed outlier: 3.959A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 40 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.665A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 111 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 150 through 177 removed outlier: 4.188A pdb=" N THR C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 238 removed outlier: 3.603A pdb=" N PHE C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 3.970A pdb=" N GLN D 15 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 40 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.680A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 111 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 150 through 177 removed outlier: 4.168A pdb=" N THR D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 238 removed outlier: 3.607A pdb=" N PHE D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 15 removed outlier: 3.984A pdb=" N GLN E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 40 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.622A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 111 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 150 through 177 removed outlier: 4.137A pdb=" N THR E 154 " --> pdb=" O GLY E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 238 removed outlier: 3.648A pdb=" N PHE E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 15 removed outlier: 3.954A pdb=" N GLN F 15 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 40 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.672A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 111 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 150 through 177 removed outlier: 4.191A pdb=" N THR F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 238 removed outlier: 3.600A pdb=" N PHE F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 738 hydrogen bonds defined for protein. 2178 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: 1.23 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2910 1.34 - 1.46: 2455 1.46 - 1.58: 5027 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 10452 Sorted by residual: bond pdb=" CA HIS A 194 " pdb=" C HIS A 194 " ideal model delta sigma weight residual 1.532 1.521 0.011 1.12e-02 7.97e+03 9.77e-01 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.28e-02 6.10e+03 9.70e-01 bond pdb=" CB PHE E 97 " pdb=" CG PHE E 97 " ideal model delta sigma weight residual 1.502 1.525 -0.023 2.30e-02 1.89e+03 9.67e-01 bond pdb=" CA HIS F 194 " pdb=" C HIS F 194 " ideal model delta sigma weight residual 1.532 1.522 0.011 1.12e-02 7.97e+03 8.97e-01 bond pdb=" C TYR C 177 " pdb=" N GLY C 178 " ideal model delta sigma weight residual 1.335 1.328 0.007 7.50e-03 1.78e+04 8.56e-01 ... (remaining 10447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 13630 1.31 - 2.61: 278 2.61 - 3.92: 69 3.92 - 5.23: 6 5.23 - 6.53: 9 Bond angle restraints: 13992 Sorted by residual: angle pdb=" C HIS A 194 " pdb=" CA HIS A 194 " pdb=" CB HIS A 194 " ideal model delta sigma weight residual 116.34 111.01 5.33 1.40e+00 5.10e-01 1.45e+01 angle pdb=" C HIS D 194 " pdb=" CA HIS D 194 " pdb=" CB HIS D 194 " ideal model delta sigma weight residual 116.34 111.03 5.31 1.40e+00 5.10e-01 1.44e+01 angle pdb=" C HIS B 194 " pdb=" CA HIS B 194 " pdb=" CB HIS B 194 " ideal model delta sigma weight residual 116.34 111.11 5.23 1.40e+00 5.10e-01 1.39e+01 angle pdb=" C HIS C 194 " pdb=" CA HIS C 194 " pdb=" CB HIS C 194 " ideal model delta sigma weight residual 116.34 111.12 5.22 1.40e+00 5.10e-01 1.39e+01 angle pdb=" C HIS E 194 " pdb=" CA HIS E 194 " pdb=" CB HIS E 194 " ideal model delta sigma weight residual 116.34 111.14 5.20 1.40e+00 5.10e-01 1.38e+01 ... (remaining 13987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 5083 11.91 - 23.81: 765 23.81 - 35.71: 239 35.71 - 47.62: 103 47.62 - 59.52: 32 Dihedral angle restraints: 6222 sinusoidal: 2694 harmonic: 3528 Sorted by residual: dihedral pdb=" CG ARG B 53 " pdb=" CD ARG B 53 " pdb=" NE ARG B 53 " pdb=" CZ ARG B 53 " ideal model delta sinusoidal sigma weight residual -90.00 -45.51 -44.49 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG E 53 " pdb=" CD ARG E 53 " pdb=" NE ARG E 53 " pdb=" CZ ARG E 53 " ideal model delta sinusoidal sigma weight residual -90.00 -45.55 -44.45 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA GLU C 42 " pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " ideal model delta sinusoidal sigma weight residual -180.00 -120.48 -59.52 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1250 0.046 - 0.093: 264 0.093 - 0.139: 20 0.139 - 0.186: 8 0.186 - 0.232: 6 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CB ILE D 225 " pdb=" CA ILE D 225 " pdb=" CG1 ILE D 225 " pdb=" CG2 ILE D 225 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 225 " pdb=" CA ILE A 225 " pdb=" CG1 ILE A 225 " pdb=" CG2 ILE A 225 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE C 225 " pdb=" CA ILE C 225 " pdb=" CG1 ILE C 225 " pdb=" CG2 ILE C 225 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1545 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 97 " -0.008 2.00e-02 2.50e+03 1.12e-02 2.21e+00 pdb=" CG PHE B 97 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE B 97 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 97 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 97 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 97 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 97 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 97 " -0.007 2.00e-02 2.50e+03 1.10e-02 2.12e+00 pdb=" CG PHE C 97 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 97 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 97 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 97 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 97 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 97 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 97 " -0.007 2.00e-02 2.50e+03 9.92e-03 1.72e+00 pdb=" CG PHE F 97 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE F 97 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE F 97 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE F 97 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 97 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 97 " 0.000 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 229 2.72 - 3.26: 9661 3.26 - 3.81: 15860 3.81 - 4.35: 16429 4.35 - 4.90: 31465 Nonbonded interactions: 73644 Sorted by model distance: nonbonded pdb=" O ILE A 72 " pdb=" OH TYR A 177 " model vdw 2.173 3.040 nonbonded pdb=" O ILE D 72 " pdb=" OH TYR D 177 " model vdw 2.176 3.040 nonbonded pdb=" O LEU E 35 " pdb=" OG1 THR E 39 " model vdw 2.231 3.040 nonbonded pdb=" O LEU B 35 " pdb=" OG1 THR B 39 " model vdw 2.239 3.040 nonbonded pdb=" O ILE B 72 " pdb=" OH TYR B 177 " model vdw 2.244 3.040 ... (remaining 73639 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 303 or (resid 304 and (name C02 or name C03 or n \ ame C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13)) or resid 305)) selection = (chain 'B' and (resid 2 through 303 or (resid 304 and (name C02 or name C03 or n \ ame C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13)) or resid 305)) selection = (chain 'C' and (resid 2 through 303 or (resid 304 and (name C02 or name C03 or n \ ame C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13)) or resid 305)) selection = (chain 'D' and (resid 2 through 303 or (resid 304 and (name C02 or name C03 or n \ ame C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13)) or resid 305)) selection = (chain 'E' and (resid 2 through 303 or (resid 304 and (name C02 or name C03 or n \ ame C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13)) or resid 305)) selection = (chain 'F' and (resid 2 through 301 or (resid 302 and (name C02 or name C03 or n \ ame C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 \ or name C11 or name C12 or name C13)) or resid 303 through 305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.880 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.023 10470 Z= 0.131 Angle : 0.488 6.533 14028 Z= 0.270 Chirality : 0.038 0.232 1548 Planarity : 0.003 0.038 1650 Dihedral : 13.710 59.525 3888 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.31 % Favored : 95.18 % Rotamer: Outliers : 0.28 % Allowed : 16.11 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.25), residues: 1182 helix: 3.15 (0.16), residues: 840 sheet: 0.40 (0.55), residues: 102 loop : -2.44 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 53 TYR 0.012 0.001 TYR C 230 PHE 0.026 0.001 PHE B 97 TRP 0.005 0.001 TRP F 45 HIS 0.002 0.001 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00269 (10452) covalent geometry : angle 0.48812 (13992) SS BOND : bond 0.00171 ( 18) SS BOND : angle 0.41972 ( 36) hydrogen bonds : bond 0.11368 ( 738) hydrogen bonds : angle 3.57371 ( 2178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 0.397 Fit side-chains REVERT: A 103 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8778 (mt-10) REVERT: A 104 GLU cc_start: 0.9329 (tp30) cc_final: 0.8965 (tm-30) REVERT: A 107 ASN cc_start: 0.8275 (t0) cc_final: 0.8038 (t0) REVERT: B 103 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8788 (mt-10) REVERT: C 103 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8566 (mt-10) REVERT: D 103 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8599 (mt-10) REVERT: D 104 GLU cc_start: 0.9340 (tp30) cc_final: 0.9130 (tm-30) REVERT: D 107 ASN cc_start: 0.8197 (t0) cc_final: 0.7931 (t0) REVERT: E 103 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8626 (mt-10) REVERT: F 103 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8576 (mt-10) outliers start: 3 outliers final: 1 residues processed: 307 average time/residue: 0.1118 time to fit residues: 46.0722 Evaluate side-chains 193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.076025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053109 restraints weight = 33752.907| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.00 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10470 Z= 0.144 Angle : 0.558 6.288 14028 Z= 0.290 Chirality : 0.036 0.144 1548 Planarity : 0.004 0.073 1650 Dihedral : 6.425 45.100 1615 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.82 % Favored : 94.67 % Rotamer: Outliers : 3.33 % Allowed : 18.52 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.25), residues: 1182 helix: 3.14 (0.16), residues: 840 sheet: 1.62 (0.62), residues: 72 loop : -1.82 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 148 TYR 0.014 0.001 TYR E 155 PHE 0.012 0.001 PHE A 32 TRP 0.018 0.001 TRP E 4 HIS 0.001 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00319 (10452) covalent geometry : angle 0.55772 (13992) SS BOND : bond 0.00101 ( 18) SS BOND : angle 0.52191 ( 36) hydrogen bonds : bond 0.04223 ( 738) hydrogen bonds : angle 2.97114 ( 2178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.8187 (t0) cc_final: 0.7288 (m-30) REVERT: A 81 GLN cc_start: 0.9446 (tt0) cc_final: 0.8666 (tp40) REVERT: A 103 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9091 (mt-10) REVERT: A 205 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8787 (mm-30) REVERT: B 76 ARG cc_start: 0.9266 (mpt180) cc_final: 0.9025 (mpt-90) REVERT: B 81 GLN cc_start: 0.9437 (OUTLIER) cc_final: 0.9236 (tt0) REVERT: B 103 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9224 (mt-10) REVERT: C 103 GLU cc_start: 0.9477 (mm-30) cc_final: 0.8951 (tp30) REVERT: C 226 ILE cc_start: 0.9650 (OUTLIER) cc_final: 0.9410 (mm) REVERT: D 81 GLN cc_start: 0.9429 (tt0) cc_final: 0.8682 (tp40) REVERT: D 103 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9122 (mt-10) REVERT: D 104 GLU cc_start: 0.9450 (tp30) cc_final: 0.9172 (tm-30) REVERT: D 205 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8803 (mm-30) REVERT: E 76 ARG cc_start: 0.9256 (mpt180) cc_final: 0.9031 (mpt-90) REVERT: E 103 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9232 (mt-10) REVERT: E 104 GLU cc_start: 0.9338 (tm-30) cc_final: 0.8673 (tm-30) REVERT: E 108 LYS cc_start: 0.9399 (tptp) cc_final: 0.9022 (mtmm) REVERT: F 103 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9166 (mm-30) REVERT: F 226 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9413 (mm) REVERT: F 229 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9183 (t80) outliers start: 36 outliers final: 17 residues processed: 237 average time/residue: 0.0878 time to fit residues: 29.5079 Evaluate side-chains 200 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 30.0000 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN C 107 ASN E 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.076026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.053235 restraints weight = 34441.605| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 4.08 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10470 Z= 0.115 Angle : 0.551 6.260 14028 Z= 0.285 Chirality : 0.035 0.141 1548 Planarity : 0.003 0.041 1650 Dihedral : 6.008 47.114 1614 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.23 % Favored : 95.26 % Rotamer: Outliers : 3.06 % Allowed : 20.00 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.25), residues: 1182 helix: 3.31 (0.16), residues: 840 sheet: 1.54 (0.61), residues: 72 loop : -1.68 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.009 0.001 TYR C 98 PHE 0.011 0.001 PHE C 32 TRP 0.007 0.001 TRP F 45 HIS 0.001 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00242 (10452) covalent geometry : angle 0.55097 (13992) SS BOND : bond 0.00092 ( 18) SS BOND : angle 0.47455 ( 36) hydrogen bonds : bond 0.03755 ( 738) hydrogen bonds : angle 2.85210 ( 2178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8363 (tp30) cc_final: 0.8155 (mm-30) REVERT: A 81 GLN cc_start: 0.9444 (tt0) cc_final: 0.9226 (tt0) REVERT: A 86 SER cc_start: 0.9608 (OUTLIER) cc_final: 0.9274 (p) REVERT: A 103 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9178 (mt-10) REVERT: A 205 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8877 (tp30) REVERT: B 76 ARG cc_start: 0.9239 (mpt180) cc_final: 0.8991 (mpt-90) REVERT: B 104 GLU cc_start: 0.9309 (tm-30) cc_final: 0.8621 (tm-30) REVERT: B 108 LYS cc_start: 0.9317 (tptp) cc_final: 0.8925 (mtmm) REVERT: B 189 ARG cc_start: 0.8149 (ttt90) cc_final: 0.7814 (ttm-80) REVERT: B 205 GLU cc_start: 0.9085 (tp30) cc_final: 0.8832 (mm-30) REVERT: C 103 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9233 (tp30) REVERT: C 205 GLU cc_start: 0.8942 (tt0) cc_final: 0.8606 (tp30) REVERT: C 226 ILE cc_start: 0.9637 (OUTLIER) cc_final: 0.9396 (mm) REVERT: C 229 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.9153 (t80) REVERT: D 62 GLU cc_start: 0.8322 (tp30) cc_final: 0.8111 (mm-30) REVERT: D 103 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9103 (mt-10) REVERT: D 104 GLU cc_start: 0.9430 (tp30) cc_final: 0.9138 (tm-30) REVERT: D 108 LYS cc_start: 0.9357 (tptp) cc_final: 0.9002 (mtmm) REVERT: D 205 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8881 (tp30) REVERT: E 76 ARG cc_start: 0.9245 (mpt180) cc_final: 0.8986 (mpt-90) REVERT: E 81 GLN cc_start: 0.9417 (tt0) cc_final: 0.8763 (tt0) REVERT: E 104 GLU cc_start: 0.9374 (tm-30) cc_final: 0.8701 (tm-30) REVERT: E 108 LYS cc_start: 0.9306 (tptp) cc_final: 0.8908 (mtmm) REVERT: E 155 TYR cc_start: 0.9528 (t80) cc_final: 0.9312 (t80) REVERT: E 189 ARG cc_start: 0.8108 (ttt90) cc_final: 0.7766 (ttm-80) REVERT: E 228 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9435 (tp) REVERT: F 205 GLU cc_start: 0.8882 (tt0) cc_final: 0.8654 (tp30) REVERT: F 226 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9411 (mm) REVERT: F 229 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.9166 (t80) outliers start: 33 outliers final: 22 residues processed: 225 average time/residue: 0.0856 time to fit residues: 27.6416 Evaluate side-chains 212 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.075990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.052018 restraints weight = 34714.912| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.14 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10470 Z= 0.123 Angle : 0.540 6.275 14028 Z= 0.281 Chirality : 0.034 0.142 1548 Planarity : 0.003 0.027 1650 Dihedral : 5.864 46.850 1614 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.31 % Favored : 95.18 % Rotamer: Outliers : 3.33 % Allowed : 20.74 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.25), residues: 1182 helix: 3.33 (0.16), residues: 840 sheet: 1.54 (0.61), residues: 72 loop : -1.58 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 189 TYR 0.009 0.001 TYR C 98 PHE 0.012 0.001 PHE D 32 TRP 0.007 0.001 TRP C 4 HIS 0.001 0.000 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00267 (10452) covalent geometry : angle 0.54004 (13992) SS BOND : bond 0.00089 ( 18) SS BOND : angle 0.42243 ( 36) hydrogen bonds : bond 0.03603 ( 738) hydrogen bonds : angle 2.89610 ( 2178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8416 (tp30) cc_final: 0.8193 (mm-30) REVERT: A 81 GLN cc_start: 0.9441 (tt0) cc_final: 0.9225 (tt0) REVERT: A 86 SER cc_start: 0.9633 (OUTLIER) cc_final: 0.9311 (p) REVERT: A 103 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9213 (mt-10) REVERT: B 81 GLN cc_start: 0.9467 (tt0) cc_final: 0.8868 (tt0) REVERT: B 205 GLU cc_start: 0.9035 (tp30) cc_final: 0.8796 (mm-30) REVERT: C 103 GLU cc_start: 0.9486 (mm-30) cc_final: 0.8984 (tp30) REVERT: C 205 GLU cc_start: 0.8893 (tt0) cc_final: 0.8566 (mm-30) REVERT: C 226 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9396 (mm) REVERT: D 62 GLU cc_start: 0.8447 (tp30) cc_final: 0.8221 (mm-30) REVERT: D 103 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9179 (pt0) REVERT: D 104 GLU cc_start: 0.9523 (tp30) cc_final: 0.9264 (tm-30) REVERT: E 76 ARG cc_start: 0.9259 (mpt180) cc_final: 0.9003 (mpt-90) REVERT: E 81 GLN cc_start: 0.9454 (tt0) cc_final: 0.8766 (tt0) REVERT: E 155 TYR cc_start: 0.9523 (t80) cc_final: 0.9239 (t80) REVERT: E 205 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8782 (mm-30) REVERT: F 205 GLU cc_start: 0.8800 (tt0) cc_final: 0.8480 (mm-30) REVERT: F 226 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9407 (mm) REVERT: F 229 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9167 (t80) outliers start: 36 outliers final: 25 residues processed: 218 average time/residue: 0.0767 time to fit residues: 24.4893 Evaluate side-chains 206 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 30.0000 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN D 107 ASN F 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.076240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.052501 restraints weight = 34156.794| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 4.06 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10470 Z= 0.120 Angle : 0.546 6.277 14028 Z= 0.286 Chirality : 0.034 0.147 1548 Planarity : 0.003 0.025 1650 Dihedral : 5.726 46.936 1614 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.89 % Favored : 95.60 % Rotamer: Outliers : 3.06 % Allowed : 22.69 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.25), residues: 1182 helix: 3.26 (0.16), residues: 852 sheet: 1.56 (0.62), residues: 72 loop : -1.41 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 76 TYR 0.009 0.001 TYR C 98 PHE 0.011 0.001 PHE A 32 TRP 0.008 0.001 TRP C 4 HIS 0.002 0.000 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00264 (10452) covalent geometry : angle 0.54658 (13992) SS BOND : bond 0.00106 ( 18) SS BOND : angle 0.39491 ( 36) hydrogen bonds : bond 0.03547 ( 738) hydrogen bonds : angle 2.87004 ( 2178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8323 (pm20) cc_final: 0.8017 (pm20) REVERT: A 62 GLU cc_start: 0.8427 (tp30) cc_final: 0.8178 (mm-30) REVERT: A 86 SER cc_start: 0.9623 (OUTLIER) cc_final: 0.9297 (p) REVERT: A 103 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9217 (mt-10) REVERT: B 81 GLN cc_start: 0.9459 (tt0) cc_final: 0.8797 (tt0) REVERT: B 205 GLU cc_start: 0.9095 (tp30) cc_final: 0.8665 (mm-30) REVERT: B 228 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9447 (tp) REVERT: C 103 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9103 (tp30) REVERT: C 205 GLU cc_start: 0.8873 (tt0) cc_final: 0.8668 (tp30) REVERT: C 226 ILE cc_start: 0.9629 (OUTLIER) cc_final: 0.9388 (mm) REVERT: D 42 GLU cc_start: 0.8349 (pm20) cc_final: 0.8053 (pm20) REVERT: D 62 GLU cc_start: 0.8473 (tp30) cc_final: 0.8213 (mm-30) REVERT: D 103 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9174 (mt-10) REVERT: D 104 GLU cc_start: 0.9445 (tp30) cc_final: 0.8981 (tm-30) REVERT: D 108 LYS cc_start: 0.9349 (tptp) cc_final: 0.8984 (mtmm) REVERT: E 42 GLU cc_start: 0.8432 (pm20) cc_final: 0.8036 (pm20) REVERT: E 81 GLN cc_start: 0.9462 (tt0) cc_final: 0.8770 (tt0) REVERT: E 104 GLU cc_start: 0.9378 (tm-30) cc_final: 0.9033 (tm-30) REVERT: E 108 LYS cc_start: 0.9399 (tptp) cc_final: 0.9128 (mmmt) REVERT: E 155 TYR cc_start: 0.9515 (t80) cc_final: 0.9309 (t80) REVERT: E 205 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8691 (mm-30) REVERT: F 81 GLN cc_start: 0.9392 (tt0) cc_final: 0.8608 (tt0) REVERT: F 205 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: F 226 ILE cc_start: 0.9641 (OUTLIER) cc_final: 0.9408 (mm) outliers start: 33 outliers final: 24 residues processed: 204 average time/residue: 0.0736 time to fit residues: 22.6286 Evaluate side-chains 204 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 0.0000 chunk 66 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 chunk 115 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.076652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.052614 restraints weight = 34669.885| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 4.15 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10470 Z= 0.112 Angle : 0.546 6.259 14028 Z= 0.284 Chirality : 0.035 0.143 1548 Planarity : 0.003 0.025 1650 Dihedral : 5.614 46.494 1614 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.59 % Allowed : 22.87 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.43 (0.25), residues: 1182 helix: 3.30 (0.16), residues: 852 sheet: 1.56 (0.62), residues: 72 loop : -1.36 (0.44), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.009 0.001 TYR C 98 PHE 0.010 0.001 PHE F 32 TRP 0.018 0.001 TRP E 4 HIS 0.001 0.000 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00232 (10452) covalent geometry : angle 0.54639 (13992) SS BOND : bond 0.00089 ( 18) SS BOND : angle 0.40321 ( 36) hydrogen bonds : bond 0.03367 ( 738) hydrogen bonds : angle 2.81888 ( 2178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9402 (tt0) cc_final: 0.8734 (tt0) REVERT: A 103 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9213 (mt-10) REVERT: B 42 GLU cc_start: 0.8446 (pm20) cc_final: 0.8076 (pm20) REVERT: B 81 GLN cc_start: 0.9446 (tt0) cc_final: 0.8778 (tt0) REVERT: B 205 GLU cc_start: 0.9090 (tp30) cc_final: 0.8696 (mm-30) REVERT: C 205 GLU cc_start: 0.8927 (tt0) cc_final: 0.8661 (tp30) REVERT: C 226 ILE cc_start: 0.9608 (OUTLIER) cc_final: 0.9382 (mm) REVERT: D 103 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9202 (pt0) REVERT: D 104 GLU cc_start: 0.9466 (tp30) cc_final: 0.9229 (tm-30) REVERT: E 155 TYR cc_start: 0.9497 (t80) cc_final: 0.9230 (t80) REVERT: E 205 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8648 (mm-30) REVERT: F 81 GLN cc_start: 0.9379 (tt0) cc_final: 0.8588 (tt0) REVERT: F 226 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9390 (mm) outliers start: 28 outliers final: 23 residues processed: 200 average time/residue: 0.0771 time to fit residues: 23.1350 Evaluate side-chains 199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.076059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.052192 restraints weight = 34515.868| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.11 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10470 Z= 0.128 Angle : 0.556 6.315 14028 Z= 0.291 Chirality : 0.035 0.142 1548 Planarity : 0.003 0.025 1650 Dihedral : 5.647 45.327 1614 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.98 % Favored : 95.52 % Rotamer: Outliers : 2.78 % Allowed : 22.96 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.39 (0.25), residues: 1182 helix: 3.27 (0.16), residues: 852 sheet: 1.45 (0.60), residues: 72 loop : -1.34 (0.44), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 148 TYR 0.012 0.001 TYR C 98 PHE 0.010 0.001 PHE F 32 TRP 0.016 0.001 TRP E 4 HIS 0.001 0.000 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00285 (10452) covalent geometry : angle 0.55625 (13992) SS BOND : bond 0.00078 ( 18) SS BOND : angle 0.43518 ( 36) hydrogen bonds : bond 0.03433 ( 738) hydrogen bonds : angle 2.90111 ( 2178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8431 (pm20) cc_final: 0.8113 (pm20) REVERT: A 81 GLN cc_start: 0.9404 (tt0) cc_final: 0.8756 (tt0) REVERT: A 103 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9197 (mt-10) REVERT: B 81 GLN cc_start: 0.9456 (tt0) cc_final: 0.8768 (tt0) REVERT: B 205 GLU cc_start: 0.9069 (tp30) cc_final: 0.8835 (mm-30) REVERT: C 81 GLN cc_start: 0.9386 (tt0) cc_final: 0.8612 (tt0) REVERT: C 205 GLU cc_start: 0.8952 (tt0) cc_final: 0.8663 (tp30) REVERT: C 226 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9376 (mm) REVERT: C 227 GLU cc_start: 0.9333 (tm-30) cc_final: 0.9093 (tm-30) REVERT: D 42 GLU cc_start: 0.8412 (pm20) cc_final: 0.8089 (pm20) REVERT: D 103 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9193 (mt-10) REVERT: D 104 GLU cc_start: 0.9456 (tp30) cc_final: 0.9235 (tm-30) REVERT: E 81 GLN cc_start: 0.9460 (tt0) cc_final: 0.8895 (tt0) REVERT: F 42 GLU cc_start: 0.8799 (pm20) cc_final: 0.8579 (pm20) REVERT: F 81 GLN cc_start: 0.9384 (tt0) cc_final: 0.8586 (tt0) REVERT: F 205 GLU cc_start: 0.9122 (tp30) cc_final: 0.8599 (mm-30) REVERT: F 226 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9378 (mm) outliers start: 30 outliers final: 22 residues processed: 200 average time/residue: 0.0711 time to fit residues: 21.0548 Evaluate side-chains 193 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.076328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.052341 restraints weight = 34284.416| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.11 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10470 Z= 0.118 Angle : 0.573 6.626 14028 Z= 0.297 Chirality : 0.035 0.143 1548 Planarity : 0.003 0.027 1650 Dihedral : 5.603 44.540 1614 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.81 % Favored : 95.69 % Rotamer: Outliers : 2.50 % Allowed : 24.17 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.25), residues: 1182 helix: 3.21 (0.16), residues: 852 sheet: 1.43 (0.60), residues: 72 loop : -1.37 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.010 0.001 TYR C 98 PHE 0.010 0.001 PHE F 32 TRP 0.014 0.001 TRP E 4 HIS 0.001 0.000 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00267 (10452) covalent geometry : angle 0.57340 (13992) SS BOND : bond 0.00086 ( 18) SS BOND : angle 0.40249 ( 36) hydrogen bonds : bond 0.03396 ( 738) hydrogen bonds : angle 2.88547 ( 2178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9398 (tt0) cc_final: 0.8739 (tt0) REVERT: A 103 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9190 (mt-10) REVERT: B 42 GLU cc_start: 0.8480 (pm20) cc_final: 0.8139 (pm20) REVERT: B 81 GLN cc_start: 0.9456 (tt0) cc_final: 0.8773 (tt0) REVERT: B 205 GLU cc_start: 0.9082 (tp30) cc_final: 0.8863 (mm-30) REVERT: C 81 GLN cc_start: 0.9393 (tt0) cc_final: 0.8616 (tt0) REVERT: C 205 GLU cc_start: 0.8940 (tt0) cc_final: 0.8665 (tp30) REVERT: C 226 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9373 (mm) REVERT: C 227 GLU cc_start: 0.9362 (tm-30) cc_final: 0.9151 (tm-30) REVERT: D 42 GLU cc_start: 0.8428 (pm20) cc_final: 0.8083 (pm20) REVERT: D 103 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9205 (pt0) REVERT: E 42 GLU cc_start: 0.8486 (pm20) cc_final: 0.8144 (pm20) REVERT: E 81 GLN cc_start: 0.9457 (tt0) cc_final: 0.8880 (tt0) REVERT: E 205 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8709 (mm-30) REVERT: F 81 GLN cc_start: 0.9379 (tt0) cc_final: 0.8580 (tt0) REVERT: F 205 GLU cc_start: 0.9134 (tp30) cc_final: 0.8885 (mm-30) REVERT: F 226 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9377 (mm) outliers start: 27 outliers final: 22 residues processed: 205 average time/residue: 0.0684 time to fit residues: 21.1416 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 61 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.052112 restraints weight = 34304.829| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.10 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10470 Z= 0.127 Angle : 0.610 7.780 14028 Z= 0.314 Chirality : 0.036 0.179 1548 Planarity : 0.003 0.032 1650 Dihedral : 5.630 43.382 1614 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.23 % Favored : 95.26 % Rotamer: Outliers : 2.41 % Allowed : 24.07 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.25), residues: 1182 helix: 3.23 (0.16), residues: 852 sheet: 1.43 (0.60), residues: 72 loop : -1.37 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 148 TYR 0.011 0.001 TYR C 98 PHE 0.010 0.001 PHE B 32 TRP 0.013 0.001 TRP E 4 HIS 0.001 0.000 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00292 (10452) covalent geometry : angle 0.61064 (13992) SS BOND : bond 0.00079 ( 18) SS BOND : angle 0.37494 ( 36) hydrogen bonds : bond 0.03413 ( 738) hydrogen bonds : angle 2.92672 ( 2178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8478 (pm20) cc_final: 0.8206 (pm20) REVERT: A 81 GLN cc_start: 0.9389 (tt0) cc_final: 0.8727 (tt0) REVERT: A 103 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9190 (mt-10) REVERT: B 81 GLN cc_start: 0.9461 (tt0) cc_final: 0.8774 (tt0) REVERT: B 205 GLU cc_start: 0.9051 (tp30) cc_final: 0.8827 (mm-30) REVERT: B 214 LEU cc_start: 0.9670 (tp) cc_final: 0.9455 (tp) REVERT: C 42 GLU cc_start: 0.8623 (pm20) cc_final: 0.8395 (pm20) REVERT: C 81 GLN cc_start: 0.9391 (tt0) cc_final: 0.8619 (tt0) REVERT: C 205 GLU cc_start: 0.8951 (tt0) cc_final: 0.8694 (tp30) REVERT: C 226 ILE cc_start: 0.9601 (OUTLIER) cc_final: 0.9385 (mm) REVERT: C 227 GLU cc_start: 0.9387 (tm-30) cc_final: 0.9183 (tm-30) REVERT: C 229 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9180 (t80) REVERT: D 103 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9190 (mt-10) REVERT: E 81 GLN cc_start: 0.9455 (tt0) cc_final: 0.8867 (tt0) REVERT: F 81 GLN cc_start: 0.9370 (tt0) cc_final: 0.8563 (tt0) REVERT: F 205 GLU cc_start: 0.9131 (tp30) cc_final: 0.8902 (mm-30) REVERT: F 226 ILE cc_start: 0.9606 (OUTLIER) cc_final: 0.9385 (mm) REVERT: F 229 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.9155 (t80) outliers start: 26 outliers final: 22 residues processed: 201 average time/residue: 0.0648 time to fit residues: 20.6253 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.052007 restraints weight = 34147.892| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.09 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10470 Z= 0.145 Angle : 0.624 7.393 14028 Z= 0.323 Chirality : 0.035 0.141 1548 Planarity : 0.003 0.024 1650 Dihedral : 5.733 42.554 1614 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.98 % Favored : 95.52 % Rotamer: Outliers : 2.41 % Allowed : 24.35 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.25), residues: 1182 helix: 3.17 (0.16), residues: 852 sheet: 1.50 (0.60), residues: 72 loop : -1.48 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 76 TYR 0.012 0.001 TYR C 98 PHE 0.010 0.001 PHE C 32 TRP 0.013 0.001 TRP A 4 HIS 0.001 0.000 HIS C 95 Details of bonding type rmsd covalent geometry : bond 0.00334 (10452) covalent geometry : angle 0.62444 (13992) SS BOND : bond 0.00090 ( 18) SS BOND : angle 0.38316 ( 36) hydrogen bonds : bond 0.03602 ( 738) hydrogen bonds : angle 3.00758 ( 2178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.317 Fit side-chains REVERT: A 42 GLU cc_start: 0.8483 (pm20) cc_final: 0.8228 (pm20) REVERT: A 81 GLN cc_start: 0.9412 (tt0) cc_final: 0.8757 (tt0) REVERT: A 103 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9197 (mt-10) REVERT: B 42 GLU cc_start: 0.8601 (pm20) cc_final: 0.8364 (pm20) REVERT: B 81 GLN cc_start: 0.9468 (tt0) cc_final: 0.8775 (tt0) REVERT: B 205 GLU cc_start: 0.9068 (tp30) cc_final: 0.8696 (mm-30) REVERT: B 214 LEU cc_start: 0.9680 (tp) cc_final: 0.9456 (tp) REVERT: C 81 GLN cc_start: 0.9407 (tt0) cc_final: 0.8618 (tt0) REVERT: C 205 GLU cc_start: 0.8994 (tt0) cc_final: 0.8710 (tp30) REVERT: C 226 ILE cc_start: 0.9598 (OUTLIER) cc_final: 0.9377 (mm) REVERT: C 229 PHE cc_start: 0.9483 (OUTLIER) cc_final: 0.9176 (t80) REVERT: D 42 GLU cc_start: 0.8458 (pm20) cc_final: 0.8222 (pm20) REVERT: D 103 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9217 (pt0) REVERT: F 81 GLN cc_start: 0.9377 (tt0) cc_final: 0.8548 (tt0) REVERT: F 155 TYR cc_start: 0.9643 (t80) cc_final: 0.9365 (t80) REVERT: F 205 GLU cc_start: 0.9122 (tp30) cc_final: 0.8820 (mm-30) REVERT: F 226 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9387 (mm) REVERT: F 229 PHE cc_start: 0.9480 (OUTLIER) cc_final: 0.9172 (t80) outliers start: 26 outliers final: 19 residues processed: 207 average time/residue: 0.0654 time to fit residues: 21.2655 Evaluate side-chains 199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.075915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.052098 restraints weight = 34742.748| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.11 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10470 Z= 0.130 Angle : 0.633 8.749 14028 Z= 0.325 Chirality : 0.035 0.141 1548 Planarity : 0.003 0.023 1650 Dihedral : 5.728 41.838 1614 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.64 % Favored : 95.85 % Rotamer: Outliers : 2.41 % Allowed : 24.54 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.25), residues: 1182 helix: 3.19 (0.16), residues: 852 sheet: 1.49 (0.59), residues: 72 loop : -1.53 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 148 TYR 0.013 0.001 TYR A 155 PHE 0.010 0.001 PHE F 32 TRP 0.012 0.001 TRP A 4 HIS 0.001 0.000 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00304 (10452) covalent geometry : angle 0.63354 (13992) SS BOND : bond 0.00077 ( 18) SS BOND : angle 0.40724 ( 36) hydrogen bonds : bond 0.03492 ( 738) hydrogen bonds : angle 2.97401 ( 2178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1555.07 seconds wall clock time: 27 minutes 34.39 seconds (1654.39 seconds total)