Starting phenix.real_space_refine on Wed Sep 17 17:39:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r23_53521/09_2025/9r23_53521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r23_53521/09_2025/9r23_53521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r23_53521/09_2025/9r23_53521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r23_53521/09_2025/9r23_53521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r23_53521/09_2025/9r23_53521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r23_53521/09_2025/9r23_53521.map" } resolution = 2.81 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= 0.001 sd= 0.023 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 60 5.16 5 C 6884 2.51 5 N 1466 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10039 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 1861 Chain: "B" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 1861 Chain: "C" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 1861 Chain: "E" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 235, 1830 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 231} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 1861 Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 172 Unusual residues: {'LFA': 14, 'RET': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 179 Unusual residues: {'LFA': 14, 'RET': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 153 Unusual residues: {'LFA': 13, 'RET': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 128 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 143 Unusual residues: {'LFA': 12, 'RET': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 153 Unusual residues: {'LFA': 13, 'RET': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 128 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 35 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 35 " occ=0.50 residue: pdb=" N AARG B 35 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 35 " occ=0.50 residue: pdb=" N AARG D 35 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 35 " occ=0.50 residue: pdb=" N AARG E 35 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 35 " occ=0.50 Time building chain proxies: 3.41, per 1000 atoms: 0.34 Number of scatterers: 10039 At special positions: 0 Unit cell: (96.976, 99.484, 77.748, 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 60 16.00 O 1629 8.00 N 1466 7.00 C 6884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 580.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 93.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 69 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.212A pdb=" N ASP A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 126 removed outlier: 4.246A pdb=" N PHE A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 151 Processing helix chain 'A' and resid 151 through 161 removed outlier: 4.049A pdb=" N GLY A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 Processing helix chain 'A' and resid 181 through 192 Processing helix chain 'A' and resid 197 through 237 removed outlier: 4.416A pdb=" N PHE A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 69 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 99 removed outlier: 4.207A pdb=" N ASP B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 126 removed outlier: 4.292A pdb=" N PHE B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 151 Processing helix chain 'B' and resid 151 through 161 removed outlier: 4.038A pdb=" N GLY B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 181 through 191 Processing helix chain 'B' and resid 197 through 237 removed outlier: 3.600A pdb=" N ILE B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 32 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 69 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 75 through 99 removed outlier: 4.204A pdb=" N ASP C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 91 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 126 removed outlier: 4.279A pdb=" N PHE C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 151 Processing helix chain 'C' and resid 151 through 161 removed outlier: 4.042A pdb=" N GLY C 161 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 178 Processing helix chain 'C' and resid 181 through 191 Processing helix chain 'C' and resid 197 through 237 removed outlier: 4.421A pdb=" N PHE C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 32 Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 99 removed outlier: 4.197A pdb=" N ASP D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE D 91 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 126 removed outlier: 4.299A pdb=" N PHE D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP D 107 " --> pdb=" O SER D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 Processing helix chain 'D' and resid 151 through 161 removed outlier: 4.048A pdb=" N GLY D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 178 removed outlier: 3.594A pdb=" N LEU D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 197 through 237 removed outlier: 4.411A pdb=" N PHE D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 32 removed outlier: 3.513A pdb=" N GLY E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 69 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 75 through 99 removed outlier: 4.206A pdb=" N ASP E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 98 " --> pdb=" O ILE E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 126 removed outlier: 4.280A pdb=" N PHE E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 Processing helix chain 'E' and resid 151 through 161 removed outlier: 4.055A pdb=" N GLY E 161 " --> pdb=" O ASN E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 178 removed outlier: 3.568A pdb=" N LEU E 174 " --> pdb=" O ASN E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 192 Processing helix chain 'E' and resid 198 through 237 removed outlier: 4.403A pdb=" N PHE E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2448 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: 1.50 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2127 1.33 - 1.45: 2638 1.45 - 1.57: 5266 1.57 - 1.69: 1 1.69 - 1.81: 115 Bond restraints: 10147 Sorted by residual: bond pdb=" CA SER B 26 " pdb=" CB SER B 26 " ideal model delta sigma weight residual 1.529 1.446 0.083 1.55e-02 4.16e+03 2.87e+01 bond pdb=" CA SER D 26 " pdb=" CB SER D 26 " ideal model delta sigma weight residual 1.529 1.447 0.082 1.55e-02 4.16e+03 2.81e+01 bond pdb=" CA SER E 26 " pdb=" CB SER E 26 " ideal model delta sigma weight residual 1.529 1.449 0.080 1.55e-02 4.16e+03 2.69e+01 bond pdb=" CA SER C 26 " pdb=" CB SER C 26 " ideal model delta sigma weight residual 1.529 1.449 0.080 1.55e-02 4.16e+03 2.68e+01 bond pdb=" CA SER A 26 " pdb=" CB SER A 26 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.55e-02 4.16e+03 2.59e+01 ... (remaining 10142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11349 2.24 - 4.47: 1817 4.47 - 6.71: 255 6.71 - 8.95: 83 8.95 - 11.19: 17 Bond angle restraints: 13521 Sorted by residual: angle pdb=" CA PHE D 218 " pdb=" CB PHE D 218 " pdb=" CG PHE D 218 " ideal model delta sigma weight residual 113.80 105.78 8.02 1.00e+00 1.00e+00 6.42e+01 angle pdb=" CA PHE B 218 " pdb=" CB PHE B 218 " pdb=" CG PHE B 218 " ideal model delta sigma weight residual 113.80 106.08 7.72 1.00e+00 1.00e+00 5.95e+01 angle pdb=" CA PHE E 218 " pdb=" CB PHE E 218 " pdb=" CG PHE E 218 " ideal model delta sigma weight residual 113.80 106.16 7.64 1.00e+00 1.00e+00 5.83e+01 angle pdb=" CA THR E 14 " pdb=" CB THR E 14 " pdb=" OG1 THR E 14 " ideal model delta sigma weight residual 109.60 98.41 11.19 1.50e+00 4.44e-01 5.56e+01 angle pdb=" CA PHE C 218 " pdb=" CB PHE C 218 " pdb=" CG PHE C 218 " ideal model delta sigma weight residual 113.80 106.37 7.43 1.00e+00 1.00e+00 5.53e+01 ... (remaining 13516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 5556 24.09 - 48.18: 251 48.18 - 72.27: 39 72.27 - 96.35: 13 96.35 - 120.44: 4 Dihedral angle restraints: 5863 sinusoidal: 2517 harmonic: 3346 Sorted by residual: dihedral pdb=" CD ARG A 33 " pdb=" NE ARG A 33 " pdb=" CZ ARG A 33 " pdb=" NH1 ARG A 33 " ideal model delta sinusoidal sigma weight residual 0.00 36.77 -36.77 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CD ARG B 33 " pdb=" NE ARG B 33 " pdb=" CZ ARG B 33 " pdb=" NH1 ARG B 33 " ideal model delta sinusoidal sigma weight residual 0.00 36.75 -36.75 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" C ARG A 173 " pdb=" N ARG A 173 " pdb=" CA ARG A 173 " pdb=" CB ARG A 173 " ideal model delta harmonic sigma weight residual -122.60 -133.43 10.83 0 2.50e+00 1.60e-01 1.88e+01 ... (remaining 5860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1063 0.082 - 0.164: 379 0.164 - 0.246: 54 0.246 - 0.328: 7 0.328 - 0.410: 1 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CA ARG A 173 " pdb=" N ARG A 173 " pdb=" C ARG A 173 " pdb=" CB ARG A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB THR A 83 " pdb=" CA THR A 83 " pdb=" OG1 THR A 83 " pdb=" CG2 THR A 83 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB THR D 83 " pdb=" CA THR D 83 " pdb=" OG1 THR D 83 " pdb=" CG2 THR D 83 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1501 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 RET D 311 " -0.092 2.00e-02 2.50e+03 9.39e-02 8.82e+01 pdb=" C11 RET D 311 " 0.081 2.00e-02 2.50e+03 pdb=" C12 RET D 311 " 0.106 2.00e-02 2.50e+03 pdb=" C13 RET D 311 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 RET E 314 " -0.092 2.00e-02 2.50e+03 9.37e-02 8.78e+01 pdb=" C11 RET E 314 " 0.082 2.00e-02 2.50e+03 pdb=" C12 RET E 314 " 0.105 2.00e-02 2.50e+03 pdb=" C13 RET E 314 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 RET A 310 " 0.091 2.00e-02 2.50e+03 9.29e-02 8.63e+01 pdb=" C11 RET A 310 " -0.081 2.00e-02 2.50e+03 pdb=" C12 RET A 310 " -0.104 2.00e-02 2.50e+03 pdb=" C13 RET A 310 " 0.094 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 690 2.71 - 3.25: 9942 3.25 - 3.80: 16405 3.80 - 4.35: 24125 4.35 - 4.90: 38383 Nonbonded interactions: 89545 Sorted by model distance: nonbonded pdb=" OH TYR C 183 " pdb=" OD1 ASP C 209 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 209 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 209 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 209 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR B 183 " pdb=" OD1 ASP B 209 " model vdw 2.174 3.040 ... (remaining 89540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 34 or resid 36 through 237 or (resid 301 and (na \ me C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 302 an \ d (name C1 or name C10 or name C11 or name C12 or name C13 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid \ 305 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name \ C7 or name C8 )))) selection = (chain 'B' and (resid 3 through 34 or resid 36 through 237 or (resid 301 and (na \ me C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 302 an \ d (name C1 or name C10 or name C11 or name C12 or name C13 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or resid 3 \ 05)) selection = (chain 'C' and (resid 3 through 34 or resid 36 through 237 or (resid 301 and (na \ me C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 302 an \ d (name C1 or name C10 or name C11 or name C12 or name C13 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid \ 305 and (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19)))) selection = (chain 'D' and (resid 3 through 34 or resid 36 through 237 or (resid 301 and (na \ me C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 302 an \ d (name C1 or name C10 or name C11 or name C12 or name C13 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (resid \ 305 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name \ C7 or name C8 )))) selection = (chain 'E' and (resid 3 through 34 or resid 36 through 237 or (resid 301 and (na \ me C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or resid 302 or \ (resid 305 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 : 0.011 0.083 10152 Z= 0.709 Angle : 1.777 11.185 13521 Z= 1.115 Chirality : 0.080 0.410 1504 Planarity : 0.023 0.323 1572 Dihedral : 14.812 120.442 3755 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.14 % Allowed : 5.35 % Favored : 91.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.21), residues: 1177 helix: -1.98 (0.13), residues: 985 sheet: None (None), residues: 0 loop : -0.33 (0.54), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.006 ARG C 231 TYR 0.031 0.007 TYR D 221 PHE 0.039 0.010 PHE E 210 TRP 0.062 0.014 TRP A 107 HIS 0.012 0.004 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.01141 (10147) covalent geometry : angle 1.77748 (13521) hydrogen bonds : bond 0.20267 ( 816) hydrogen bonds : angle 8.54304 ( 2448) Misc. bond : bond 0.03417 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.385 Fit side-chains REVERT: A 213 LYS cc_start: 0.8674 (mttp) cc_final: 0.8407 (mtpm) REVERT: B 51 MET cc_start: 0.8886 (mmp) cc_final: 0.8598 (mmt) REVERT: B 70 LYS cc_start: 0.8126 (mttt) cc_final: 0.7844 (mtmm) REVERT: B 128 MET cc_start: 0.9188 (ptt) cc_final: 0.8958 (ptm) REVERT: B 150 MET cc_start: 0.8753 (mtp) cc_final: 0.8480 (ptp) REVERT: B 167 MET cc_start: 0.7957 (mmm) cc_final: 0.7754 (mpp) REVERT: B 213 LYS cc_start: 0.8699 (mttp) cc_final: 0.8314 (mtpm) REVERT: C 51 MET cc_start: 0.8859 (mmp) cc_final: 0.8366 (mmt) REVERT: C 70 LYS cc_start: 0.8082 (mttt) cc_final: 0.7808 (mtmm) REVERT: C 167 MET cc_start: 0.7888 (mmm) cc_final: 0.7688 (mpp) REVERT: C 213 LYS cc_start: 0.8724 (mttp) cc_final: 0.8334 (mtpm) REVERT: D 70 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7633 (mtmm) REVERT: D 167 MET cc_start: 0.7990 (mmm) cc_final: 0.7620 (mpp) REVERT: D 213 LYS cc_start: 0.8724 (mttp) cc_final: 0.8335 (mtpm) REVERT: E 70 LYS cc_start: 0.7871 (mmmm) cc_final: 0.7365 (mtmm) REVERT: E 167 MET cc_start: 0.7918 (mmm) cc_final: 0.7588 (mpp) REVERT: E 213 LYS cc_start: 0.8768 (mttp) cc_final: 0.8407 (mtpm) outliers start: 29 outliers final: 9 residues processed: 159 average time/residue: 0.5535 time to fit residues: 94.2887 Evaluate side-chains 121 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 159 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS B 166 HIS C 166 HIS D 166 HIS E 34 ASN E 166 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.087885 restraints weight = 25287.082| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.18 r_work: 0.2906 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10152 Z= 0.139 Angle : 0.518 6.833 13521 Z= 0.280 Chirality : 0.037 0.116 1504 Planarity : 0.004 0.038 1572 Dihedral : 11.286 104.387 1854 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.26 % Allowed : 8.91 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.24), residues: 1177 helix: 1.26 (0.16), residues: 985 sheet: None (None), residues: 0 loop : 1.06 (0.53), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 39 TYR 0.020 0.002 TYR B 183 PHE 0.014 0.002 PHE A 15 TRP 0.014 0.001 TRP E 107 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00296 (10147) covalent geometry : angle 0.51772 (13521) hydrogen bonds : bond 0.05295 ( 816) hydrogen bonds : angle 4.53909 ( 2448) Misc. bond : bond 0.00009 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8336 (mttt) cc_final: 0.8058 (mtmm) REVERT: B 128 MET cc_start: 0.9387 (ptt) cc_final: 0.9080 (ptm) REVERT: B 167 MET cc_start: 0.8012 (mmm) cc_final: 0.7644 (mpp) REVERT: B 213 LYS cc_start: 0.8501 (mttp) cc_final: 0.8131 (mtpm) REVERT: C 70 LYS cc_start: 0.8491 (mttt) cc_final: 0.7936 (mtmm) REVERT: C 167 MET cc_start: 0.7978 (mmm) cc_final: 0.7703 (mpp) REVERT: C 213 LYS cc_start: 0.8548 (mttp) cc_final: 0.8229 (mtpm) REVERT: D 70 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7772 (mtmm) REVERT: D 167 MET cc_start: 0.8057 (mmm) cc_final: 0.7511 (mpp) REVERT: D 213 LYS cc_start: 0.8579 (mttp) cc_final: 0.8151 (mtpm) REVERT: E 70 LYS cc_start: 0.7934 (mmmm) cc_final: 0.7524 (mtmm) REVERT: E 167 MET cc_start: 0.8163 (mmm) cc_final: 0.7882 (mpp) REVERT: E 213 LYS cc_start: 0.8528 (mttp) cc_final: 0.8149 (mtpm) outliers start: 10 outliers final: 6 residues processed: 125 average time/residue: 0.5573 time to fit residues: 74.8186 Evaluate side-chains 105 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 34 ASN C 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.088446 restraints weight = 28108.265| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.39 r_work: 0.2900 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10152 Z= 0.118 Angle : 0.451 8.292 13521 Z= 0.240 Chirality : 0.036 0.117 1504 Planarity : 0.004 0.034 1572 Dihedral : 9.249 81.091 1847 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.10 % Allowed : 9.22 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.25), residues: 1177 helix: 2.31 (0.17), residues: 985 sheet: None (None), residues: 0 loop : 1.26 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 33 TYR 0.016 0.001 TYR D 187 PHE 0.012 0.002 PHE B 216 TRP 0.011 0.001 TRP B 107 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00250 (10147) covalent geometry : angle 0.45118 (13521) hydrogen bonds : bond 0.04456 ( 816) hydrogen bonds : angle 4.15243 ( 2448) Misc. bond : bond 0.00012 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8459 (mttt) cc_final: 0.8073 (mtmm) REVERT: B 128 MET cc_start: 0.9394 (ptt) cc_final: 0.9099 (ptm) REVERT: B 159 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: B 167 MET cc_start: 0.8046 (mmm) cc_final: 0.7727 (mpp) REVERT: C 70 LYS cc_start: 0.8511 (mttt) cc_final: 0.7937 (mtmm) REVERT: C 167 MET cc_start: 0.7937 (mmm) cc_final: 0.7657 (mpp) REVERT: D 70 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7292 (ptmt) REVERT: D 159 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6150 (mp0) REVERT: D 167 MET cc_start: 0.8024 (mmm) cc_final: 0.7475 (mpp) REVERT: E 70 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7472 (mtmm) REVERT: E 167 MET cc_start: 0.8144 (mmm) cc_final: 0.7893 (mpp) REVERT: E 182 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7533 (mt) outliers start: 18 outliers final: 6 residues processed: 125 average time/residue: 0.6322 time to fit residues: 84.6053 Evaluate side-chains 106 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 182 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 42 optimal weight: 0.0060 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.084314 restraints weight = 30193.763| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.38 r_work: 0.2818 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10152 Z= 0.170 Angle : 0.479 5.559 13521 Z= 0.259 Chirality : 0.038 0.115 1504 Planarity : 0.004 0.042 1572 Dihedral : 9.303 58.808 1845 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.10 % Allowed : 9.54 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.11 (0.25), residues: 1177 helix: 2.26 (0.17), residues: 985 sheet: None (None), residues: 0 loop : 1.19 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 33 TYR 0.014 0.002 TYR B 183 PHE 0.014 0.002 PHE D 218 TRP 0.014 0.001 TRP D 107 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00405 (10147) covalent geometry : angle 0.47945 (13521) hydrogen bonds : bond 0.05150 ( 816) hydrogen bonds : angle 4.22476 ( 2448) Misc. bond : bond 0.00039 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8511 (mttt) cc_final: 0.8147 (mtmm) REVERT: B 128 MET cc_start: 0.9454 (ptt) cc_final: 0.9123 (ptm) REVERT: B 159 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: B 167 MET cc_start: 0.8082 (mmm) cc_final: 0.7741 (mpp) REVERT: C 70 LYS cc_start: 0.8513 (mttt) cc_final: 0.7986 (mtmm) REVERT: C 167 MET cc_start: 0.7974 (mmm) cc_final: 0.7635 (mpp) REVERT: C 182 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7348 (mp) REVERT: D 70 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7336 (ptmt) REVERT: D 167 MET cc_start: 0.8105 (mmm) cc_final: 0.7570 (mpp) REVERT: E 70 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7506 (mtmm) REVERT: E 167 MET cc_start: 0.8143 (mmm) cc_final: 0.7892 (mpp) REVERT: E 182 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7628 (mt) outliers start: 18 outliers final: 8 residues processed: 113 average time/residue: 0.6588 time to fit residues: 79.2704 Evaluate side-chains 103 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.085207 restraints weight = 28610.813| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.39 r_work: 0.2878 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10152 Z= 0.136 Angle : 0.436 5.031 13521 Z= 0.238 Chirality : 0.036 0.115 1504 Planarity : 0.004 0.033 1572 Dihedral : 9.006 58.685 1845 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.31 % Allowed : 10.27 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.33 (0.25), residues: 1177 helix: 2.43 (0.17), residues: 985 sheet: None (None), residues: 0 loop : 1.12 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 33 TYR 0.013 0.001 TYR A 187 PHE 0.011 0.002 PHE D 218 TRP 0.011 0.001 TRP E 107 HIS 0.003 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00311 (10147) covalent geometry : angle 0.43554 (13521) hydrogen bonds : bond 0.04642 ( 816) hydrogen bonds : angle 4.11826 ( 2448) Misc. bond : bond 0.00018 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.347 Fit side-chains REVERT: A 182 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7688 (mp) REVERT: B 70 LYS cc_start: 0.8524 (mttt) cc_final: 0.8165 (mtmm) REVERT: B 128 MET cc_start: 0.9438 (ptt) cc_final: 0.9102 (ptm) REVERT: B 167 MET cc_start: 0.8088 (mmm) cc_final: 0.7747 (mpp) REVERT: C 70 LYS cc_start: 0.8540 (mttt) cc_final: 0.8024 (mtmm) REVERT: C 167 MET cc_start: 0.8002 (mmm) cc_final: 0.7781 (mpp) REVERT: C 182 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7355 (mp) REVERT: D 70 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7327 (ptmt) REVERT: D 167 MET cc_start: 0.8104 (mmm) cc_final: 0.7604 (mpp) REVERT: E 70 LYS cc_start: 0.7974 (mmmm) cc_final: 0.7532 (mtmm) REVERT: E 167 MET cc_start: 0.8160 (mmm) cc_final: 0.7955 (mpp) REVERT: E 182 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7635 (mt) outliers start: 20 outliers final: 8 residues processed: 116 average time/residue: 0.6310 time to fit residues: 78.2824 Evaluate side-chains 103 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 162 ASN D 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.088427 restraints weight = 29992.734| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.23 r_work: 0.2892 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10152 Z= 0.122 Angle : 0.418 4.671 13521 Z= 0.229 Chirality : 0.036 0.114 1504 Planarity : 0.003 0.033 1572 Dihedral : 8.696 58.248 1845 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.20 % Allowed : 10.48 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.25), residues: 1177 helix: 2.53 (0.17), residues: 990 sheet: None (None), residues: 0 loop : 1.37 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 33 TYR 0.013 0.001 TYR A 187 PHE 0.011 0.001 PHE B 216 TRP 0.010 0.001 TRP D 107 HIS 0.002 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00273 (10147) covalent geometry : angle 0.41799 (13521) hydrogen bonds : bond 0.04406 ( 816) hydrogen bonds : angle 4.04497 ( 2448) Misc. bond : bond 0.00014 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7683 (mp) REVERT: B 44 MET cc_start: 0.9121 (mmm) cc_final: 0.8865 (mmp) REVERT: B 70 LYS cc_start: 0.8500 (mttt) cc_final: 0.8139 (mtmm) REVERT: B 128 MET cc_start: 0.9444 (ptt) cc_final: 0.9122 (ptm) REVERT: B 167 MET cc_start: 0.8056 (mmm) cc_final: 0.7698 (mpp) REVERT: C 62 GLN cc_start: 0.8710 (pp30) cc_final: 0.8477 (pp30) REVERT: C 70 LYS cc_start: 0.8504 (mttt) cc_final: 0.7966 (mtmm) REVERT: C 167 MET cc_start: 0.7908 (mmm) cc_final: 0.7676 (mpp) REVERT: C 182 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7318 (mp) REVERT: C 213 LYS cc_start: 0.8430 (mttp) cc_final: 0.8084 (mtpm) REVERT: D 70 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7251 (ptmt) REVERT: D 167 MET cc_start: 0.8030 (mmm) cc_final: 0.7513 (mpp) REVERT: E 70 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7480 (mtmm) REVERT: E 167 MET cc_start: 0.8046 (mmm) cc_final: 0.7825 (mpp) outliers start: 20 outliers final: 9 residues processed: 113 average time/residue: 0.7123 time to fit residues: 85.6593 Evaluate side-chains 105 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 92 optimal weight: 0.0030 chunk 95 optimal weight: 0.8980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.085752 restraints weight = 28764.346| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.42 r_work: 0.2856 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10152 Z= 0.126 Angle : 0.421 4.610 13521 Z= 0.229 Chirality : 0.036 0.114 1504 Planarity : 0.003 0.033 1572 Dihedral : 8.647 58.619 1845 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 1.78 % Allowed : 11.22 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.58 (0.25), residues: 1177 helix: 2.57 (0.17), residues: 990 sheet: None (None), residues: 0 loop : 1.36 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 231 TYR 0.012 0.001 TYR A 187 PHE 0.011 0.001 PHE D 218 TRP 0.010 0.001 TRP D 107 HIS 0.002 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00283 (10147) covalent geometry : angle 0.42074 (13521) hydrogen bonds : bond 0.04449 ( 816) hydrogen bonds : angle 4.02679 ( 2448) Misc. bond : bond 0.00013 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.363 Fit side-chains REVERT: A 6 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6184 (mm) REVERT: A 182 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 70 LYS cc_start: 0.8447 (mttt) cc_final: 0.8063 (mtmm) REVERT: B 128 MET cc_start: 0.9454 (ptt) cc_final: 0.9093 (ptm) REVERT: B 167 MET cc_start: 0.8005 (mmm) cc_final: 0.7636 (mpp) REVERT: C 62 GLN cc_start: 0.8670 (pp30) cc_final: 0.8430 (pp30) REVERT: C 70 LYS cc_start: 0.8483 (mttt) cc_final: 0.7919 (mtmm) REVERT: C 167 MET cc_start: 0.7859 (mmm) cc_final: 0.7620 (mpp) REVERT: C 213 LYS cc_start: 0.8389 (mttp) cc_final: 0.8033 (mtpm) REVERT: D 39 ARG cc_start: 0.8564 (ptm160) cc_final: 0.8345 (ptm160) REVERT: D 70 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7201 (ptmt) REVERT: D 159 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: D 167 MET cc_start: 0.7981 (mmm) cc_final: 0.7465 (mpp) REVERT: D 182 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7406 (mp) REVERT: E 70 LYS cc_start: 0.7890 (mmmm) cc_final: 0.7411 (mtmm) REVERT: E 167 MET cc_start: 0.8026 (mmm) cc_final: 0.7794 (mpp) REVERT: E 182 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7580 (mt) REVERT: E 213 LYS cc_start: 0.8369 (mttp) cc_final: 0.8039 (mtpm) outliers start: 16 outliers final: 8 residues processed: 117 average time/residue: 0.6783 time to fit residues: 84.6185 Evaluate side-chains 110 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.2980 chunk 81 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.090380 restraints weight = 36778.177| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.70 r_work: 0.2896 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10152 Z= 0.114 Angle : 0.411 6.066 13521 Z= 0.224 Chirality : 0.035 0.113 1504 Planarity : 0.003 0.033 1572 Dihedral : 8.335 57.592 1845 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.78 % Allowed : 11.74 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.71 (0.25), residues: 1177 helix: 2.66 (0.17), residues: 990 sheet: None (None), residues: 0 loop : 1.39 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.013 0.001 TYR A 187 PHE 0.011 0.001 PHE D 216 TRP 0.009 0.001 TRP D 107 HIS 0.002 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00248 (10147) covalent geometry : angle 0.41118 (13521) hydrogen bonds : bond 0.04225 ( 816) hydrogen bonds : angle 3.96163 ( 2448) Misc. bond : bond 0.00007 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.9084 (mmm) cc_final: 0.8807 (mmp) REVERT: B 70 LYS cc_start: 0.8485 (mttt) cc_final: 0.8156 (mtmm) REVERT: B 128 MET cc_start: 0.9387 (ptt) cc_final: 0.9081 (ptm) REVERT: B 167 MET cc_start: 0.8017 (mmm) cc_final: 0.7670 (mpp) REVERT: C 62 GLN cc_start: 0.8654 (pp30) cc_final: 0.8449 (pp30) REVERT: C 70 LYS cc_start: 0.8548 (mttt) cc_final: 0.8045 (mtmm) REVERT: C 167 MET cc_start: 0.7873 (mmm) cc_final: 0.7656 (mpp) REVERT: C 213 LYS cc_start: 0.8378 (mttp) cc_final: 0.8074 (mtpm) REVERT: D 39 ARG cc_start: 0.8509 (ptm160) cc_final: 0.8292 (ptm160) REVERT: D 70 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7305 (ptmt) REVERT: D 159 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: D 167 MET cc_start: 0.7959 (mmm) cc_final: 0.7479 (mpp) REVERT: E 70 LYS cc_start: 0.7942 (mmmm) cc_final: 0.7553 (mtmm) REVERT: E 167 MET cc_start: 0.8016 (mmm) cc_final: 0.7808 (mpp) REVERT: E 182 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7668 (mt) REVERT: E 213 LYS cc_start: 0.8357 (mttp) cc_final: 0.8090 (mtpm) outliers start: 16 outliers final: 8 residues processed: 117 average time/residue: 0.6695 time to fit residues: 83.4582 Evaluate side-chains 106 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.111106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.086620 restraints weight = 36903.530| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.40 r_work: 0.2807 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10152 Z= 0.208 Angle : 0.509 5.023 13521 Z= 0.272 Chirality : 0.039 0.119 1504 Planarity : 0.004 0.046 1572 Dihedral : 9.892 58.579 1845 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.68 % Allowed : 12.16 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.25), residues: 1177 helix: 2.25 (0.17), residues: 990 sheet: None (None), residues: 0 loop : 1.30 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 33 TYR 0.016 0.002 TYR B 183 PHE 0.018 0.002 PHE C 218 TRP 0.012 0.002 TRP B 107 HIS 0.004 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00507 (10147) covalent geometry : angle 0.50919 (13521) hydrogen bonds : bond 0.05388 ( 816) hydrogen bonds : angle 4.20279 ( 2448) Misc. bond : bond 0.00054 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8497 (mttt) cc_final: 0.8132 (mtmm) REVERT: B 128 MET cc_start: 0.9459 (ptt) cc_final: 0.9101 (ptm) REVERT: B 167 MET cc_start: 0.8104 (mmm) cc_final: 0.7756 (mpp) REVERT: C 70 LYS cc_start: 0.8496 (mttt) cc_final: 0.7961 (mtmm) REVERT: C 167 MET cc_start: 0.7964 (mmm) cc_final: 0.7727 (mpp) REVERT: D 39 ARG cc_start: 0.8626 (ptm160) cc_final: 0.8420 (ptm160) REVERT: D 70 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7248 (ptmt) REVERT: D 159 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: D 167 MET cc_start: 0.8100 (mmm) cc_final: 0.7568 (mpp) REVERT: E 70 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7528 (mtmm) REVERT: E 167 MET cc_start: 0.8129 (mmm) cc_final: 0.7877 (mpp) REVERT: E 182 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7513 (mp) outliers start: 15 outliers final: 9 residues processed: 114 average time/residue: 0.7429 time to fit residues: 89.9011 Evaluate side-chains 106 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.087275 restraints weight = 28771.299| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.45 r_work: 0.2895 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10152 Z= 0.109 Angle : 0.412 5.476 13521 Z= 0.225 Chirality : 0.036 0.115 1504 Planarity : 0.003 0.032 1572 Dihedral : 8.772 59.142 1845 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 1.26 % Allowed : 12.58 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.25), residues: 1177 helix: 2.63 (0.17), residues: 990 sheet: None (None), residues: 0 loop : 1.36 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 33 TYR 0.015 0.001 TYR B 183 PHE 0.012 0.001 PHE A 216 TRP 0.008 0.001 TRP E 107 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00228 (10147) covalent geometry : angle 0.41195 (13521) hydrogen bonds : bond 0.04190 ( 816) hydrogen bonds : angle 3.96363 ( 2448) Misc. bond : bond 0.00006 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.9087 (mmm) cc_final: 0.8806 (mmp) REVERT: B 70 LYS cc_start: 0.8475 (mttt) cc_final: 0.8129 (mtmm) REVERT: B 128 MET cc_start: 0.9411 (ptt) cc_final: 0.9097 (ptm) REVERT: B 167 MET cc_start: 0.7980 (mmm) cc_final: 0.7632 (mpp) REVERT: C 62 GLN cc_start: 0.8634 (pp30) cc_final: 0.8428 (pp30) REVERT: C 70 LYS cc_start: 0.8514 (mttt) cc_final: 0.8004 (mtmm) REVERT: C 167 MET cc_start: 0.7834 (mmm) cc_final: 0.7617 (mpp) REVERT: C 213 LYS cc_start: 0.8332 (mttp) cc_final: 0.8028 (mtpm) REVERT: D 39 ARG cc_start: 0.8472 (ptm160) cc_final: 0.8248 (ptm160) REVERT: D 70 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7287 (ptmt) REVERT: D 159 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: D 167 MET cc_start: 0.7934 (mmm) cc_final: 0.7455 (mpp) REVERT: E 70 LYS cc_start: 0.7935 (mmmm) cc_final: 0.7516 (mtmm) REVERT: E 167 MET cc_start: 0.7977 (mmm) cc_final: 0.7737 (mpp) REVERT: E 182 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7648 (mt) outliers start: 11 outliers final: 8 residues processed: 111 average time/residue: 0.6818 time to fit residues: 80.4983 Evaluate side-chains 107 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 92 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.087751 restraints weight = 33159.766| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.53 r_work: 0.2872 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10152 Z= 0.113 Angle : 0.415 4.943 13521 Z= 0.226 Chirality : 0.036 0.114 1504 Planarity : 0.003 0.032 1572 Dihedral : 8.489 58.837 1845 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 1.47 % Allowed : 13.00 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.72 (0.25), residues: 1177 helix: 2.68 (0.17), residues: 990 sheet: None (None), residues: 0 loop : 1.34 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 33 TYR 0.014 0.001 TYR C 183 PHE 0.011 0.001 PHE A 216 TRP 0.008 0.001 TRP D 107 HIS 0.002 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00243 (10147) covalent geometry : angle 0.41524 (13521) hydrogen bonds : bond 0.04220 ( 816) hydrogen bonds : angle 3.94803 ( 2448) Misc. bond : bond 0.00007 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.72 seconds wall clock time: 59 minutes 17.21 seconds (3557.21 seconds total)