Starting phenix.real_space_refine on Sun Aug 24 23:10:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy6_42793/08_2025/8uy6_42793_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy6_42793/08_2025/8uy6_42793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uy6_42793/08_2025/8uy6_42793_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy6_42793/08_2025/8uy6_42793_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uy6_42793/08_2025/8uy6_42793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy6_42793/08_2025/8uy6_42793.map" } resolution = 1.9 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 104 5.16 5 C 14712 2.51 5 N 3728 2.21 5 O 4056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22616 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1787 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "B" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "C" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1787 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "D" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1787 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "F" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1787 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1787 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "J" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1787 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "M" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1787 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1787 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "P" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.24 Number of scatterers: 22616 At special positions: 0 Unit cell: (104, 104, 157.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 16 15.00 O 4056 8.00 N 3728 7.00 C 14712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 24 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 100 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 100 " distance=2.03 Simple disulfide: pdb=" SG CYS P 24 " - pdb=" SG CYS P 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 917.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5088 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 24 sheets defined 57.7% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 Processing helix chain 'A' and resid 34 through 59 removed outlier: 3.574A pdb=" N VAL A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 80 through 104 Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 130 through 153 Processing helix chain 'A' and resid 161 through 182 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.567A pdb=" N VAL A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.696A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 226 Proline residue: A 212 - end of helix Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.768A pdb=" N ALA B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'C' and resid 2 through 26 Processing helix chain 'C' and resid 34 through 59 removed outlier: 3.575A pdb=" N VAL C 47 " --> pdb=" O PHE C 43 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 80 through 104 Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 121 through 125 Processing helix chain 'C' and resid 130 through 153 Processing helix chain 'C' and resid 161 through 182 Proline residue: C 179 - end of helix Processing helix chain 'C' and resid 186 through 198 removed outlier: 3.569A pdb=" N VAL C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.696A pdb=" N GLU C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 226 Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'D' and resid 30 through 36 removed outlier: 3.764A pdb=" N ALA D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'E' and resid 2 through 26 Processing helix chain 'E' and resid 34 through 59 removed outlier: 3.574A pdb=" N VAL E 47 " --> pdb=" O PHE E 43 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 80 through 104 Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'E' and resid 121 through 125 Processing helix chain 'E' and resid 130 through 153 Processing helix chain 'E' and resid 161 through 182 Proline residue: E 179 - end of helix Processing helix chain 'E' and resid 186 through 198 removed outlier: 3.568A pdb=" N VAL E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.696A pdb=" N GLU E 203 " --> pdb=" O GLY E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 226 Proline residue: E 212 - end of helix Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'F' and resid 30 through 36 removed outlier: 3.764A pdb=" N ALA F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'G' and resid 2 through 26 Processing helix chain 'G' and resid 34 through 59 removed outlier: 3.575A pdb=" N VAL G 47 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS G 56 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'G' and resid 80 through 104 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 121 through 125 Processing helix chain 'G' and resid 130 through 153 Processing helix chain 'G' and resid 161 through 182 Proline residue: G 179 - end of helix Processing helix chain 'G' and resid 186 through 198 removed outlier: 3.567A pdb=" N VAL G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE G 196 " --> pdb=" O ALA G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 204 removed outlier: 3.695A pdb=" N GLU G 203 " --> pdb=" O GLY G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 226 Proline residue: G 212 - end of helix Processing helix chain 'G' and resid 230 through 241 Processing helix chain 'H' and resid 30 through 36 removed outlier: 3.764A pdb=" N ALA H 36 " --> pdb=" O SER H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 95 Processing helix chain 'I' and resid 2 through 26 Processing helix chain 'I' and resid 34 through 59 removed outlier: 3.574A pdb=" N VAL I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS I 56 " --> pdb=" O PHE I 52 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE I 57 " --> pdb=" O ALA I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 73 Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'I' and resid 80 through 104 Processing helix chain 'I' and resid 110 through 115 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 130 through 153 Processing helix chain 'I' and resid 161 through 182 Proline residue: I 179 - end of helix Processing helix chain 'I' and resid 186 through 198 removed outlier: 3.568A pdb=" N VAL I 193 " --> pdb=" O ARG I 189 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE I 196 " --> pdb=" O ALA I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 204 removed outlier: 3.697A pdb=" N GLU I 203 " --> pdb=" O GLY I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 226 Proline residue: I 212 - end of helix Processing helix chain 'I' and resid 230 through 241 Processing helix chain 'J' and resid 30 through 36 removed outlier: 3.764A pdb=" N ALA J 36 " --> pdb=" O SER J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'K' and resid 2 through 26 Processing helix chain 'K' and resid 34 through 59 removed outlier: 3.576A pdb=" N VAL K 47 " --> pdb=" O PHE K 43 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS K 56 " --> pdb=" O PHE K 52 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 73 Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'K' and resid 80 through 104 Processing helix chain 'K' and resid 110 through 115 Processing helix chain 'K' and resid 121 through 125 Processing helix chain 'K' and resid 130 through 153 Processing helix chain 'K' and resid 161 through 182 Proline residue: K 179 - end of helix Processing helix chain 'K' and resid 186 through 198 removed outlier: 3.569A pdb=" N VAL K 193 " --> pdb=" O ARG K 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE K 196 " --> pdb=" O ALA K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 204 removed outlier: 3.696A pdb=" N GLU K 203 " --> pdb=" O GLY K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 226 Proline residue: K 212 - end of helix Processing helix chain 'K' and resid 230 through 241 Processing helix chain 'L' and resid 30 through 36 removed outlier: 3.764A pdb=" N ALA L 36 " --> pdb=" O SER L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'M' and resid 2 through 26 Processing helix chain 'M' and resid 34 through 59 removed outlier: 3.574A pdb=" N VAL M 47 " --> pdb=" O PHE M 43 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 73 Processing helix chain 'M' and resid 77 through 79 No H-bonds generated for 'chain 'M' and resid 77 through 79' Processing helix chain 'M' and resid 80 through 104 Processing helix chain 'M' and resid 110 through 115 Processing helix chain 'M' and resid 121 through 125 Processing helix chain 'M' and resid 130 through 153 Processing helix chain 'M' and resid 161 through 182 Proline residue: M 179 - end of helix Processing helix chain 'M' and resid 186 through 198 removed outlier: 3.568A pdb=" N VAL M 193 " --> pdb=" O ARG M 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE M 196 " --> pdb=" O ALA M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 204 removed outlier: 3.696A pdb=" N GLU M 203 " --> pdb=" O GLY M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 226 Proline residue: M 212 - end of helix Processing helix chain 'M' and resid 230 through 241 Processing helix chain 'N' and resid 30 through 36 removed outlier: 3.767A pdb=" N ALA N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 95 Processing helix chain 'O' and resid 2 through 26 Processing helix chain 'O' and resid 34 through 59 removed outlier: 3.576A pdb=" N VAL O 47 " --> pdb=" O PHE O 43 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS O 56 " --> pdb=" O PHE O 52 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 73 Processing helix chain 'O' and resid 77 through 79 No H-bonds generated for 'chain 'O' and resid 77 through 79' Processing helix chain 'O' and resid 80 through 104 Processing helix chain 'O' and resid 110 through 115 Processing helix chain 'O' and resid 121 through 125 Processing helix chain 'O' and resid 130 through 153 Processing helix chain 'O' and resid 161 through 182 Proline residue: O 179 - end of helix Processing helix chain 'O' and resid 186 through 198 removed outlier: 3.568A pdb=" N VAL O 193 " --> pdb=" O ARG O 189 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE O 196 " --> pdb=" O ALA O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 199 through 204 removed outlier: 3.697A pdb=" N GLU O 203 " --> pdb=" O GLY O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 226 Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 230 through 241 Processing helix chain 'P' and resid 30 through 36 removed outlier: 3.764A pdb=" N ALA P 36 " --> pdb=" O SER P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 95 Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.505A pdb=" N SER B 23 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY B 12 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 54 " --> pdb=" O TRP B 41 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG B 43 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET B 52 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY B 12 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.503A pdb=" N SER D 23 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY D 12 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 54 " --> pdb=" O TRP D 41 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG D 43 " --> pdb=" O MET D 52 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N MET D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY D 12 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 9 removed outlier: 3.505A pdb=" N SER F 23 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY F 12 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 54 " --> pdb=" O TRP F 41 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG F 43 " --> pdb=" O MET F 52 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N MET F 52 " --> pdb=" O ARG F 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY F 12 " --> pdb=" O THR F 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.505A pdb=" N SER H 23 " --> pdb=" O SER H 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 12 through 14 removed outlier: 6.306A pdb=" N GLY H 12 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG H 43 " --> pdb=" O MET H 52 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 12 through 14 removed outlier: 6.306A pdb=" N GLY H 12 " --> pdb=" O THR H 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 5 through 9 removed outlier: 3.504A pdb=" N SER J 23 " --> pdb=" O SER J 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY J 12 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA J 54 " --> pdb=" O TRP J 41 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG J 43 " --> pdb=" O MET J 52 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N MET J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY J 12 " --> pdb=" O THR J 121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 5 through 9 removed outlier: 3.503A pdb=" N SER L 23 " --> pdb=" O SER L 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.306A pdb=" N GLY L 12 " --> pdb=" O THR L 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA L 54 " --> pdb=" O TRP L 41 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ARG L 43 " --> pdb=" O MET L 52 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N MET L 52 " --> pdb=" O ARG L 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.306A pdb=" N GLY L 12 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 5 through 9 removed outlier: 3.505A pdb=" N SER N 23 " --> pdb=" O SER N 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 12 through 14 removed outlier: 6.306A pdb=" N GLY N 12 " --> pdb=" O THR N 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA N 54 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG N 43 " --> pdb=" O MET N 52 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET N 52 " --> pdb=" O ARG N 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 12 through 14 removed outlier: 6.306A pdb=" N GLY N 12 " --> pdb=" O THR N 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 5 through 9 removed outlier: 3.504A pdb=" N SER P 23 " --> pdb=" O SER P 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY P 12 " --> pdb=" O THR P 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA P 54 " --> pdb=" O TRP P 41 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG P 43 " --> pdb=" O MET P 52 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N MET P 52 " --> pdb=" O ARG P 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 12 through 14 removed outlier: 6.307A pdb=" N GLY P 12 " --> pdb=" O THR P 121 " (cutoff:3.500A) 1465 hydrogen bonds defined for protein. 4107 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: 4.79 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3673 1.32 - 1.44: 6179 1.44 - 1.56: 13052 1.56 - 1.69: 32 1.69 - 1.81: 176 Bond restraints: 23112 Sorted by residual: bond pdb=" CB ASN P 89 " pdb=" CG ASN P 89 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.41e-01 bond pdb=" CB ASN N 89 " pdb=" CG ASN N 89 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.29e-01 bond pdb=" CB ASN B 89 " pdb=" CG ASN B 89 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.27e-01 bond pdb=" CB ASN D 89 " pdb=" CG ASN D 89 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.70e-01 bond pdb=" CB ASN J 89 " pdb=" CG ASN J 89 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.70e-01 ... (remaining 23107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 30727 1.70 - 3.39: 385 3.39 - 5.09: 64 5.09 - 6.78: 32 6.78 - 8.48: 8 Bond angle restraints: 31216 Sorted by residual: angle pdb=" CB2 CDL O 301 " pdb=" C1 CDL O 301 " pdb=" CA2 CDL O 301 " ideal model delta sigma weight residual 113.28 104.80 8.48 3.06e+00 1.07e-01 7.66e+00 angle pdb=" CB2 CDL G 301 " pdb=" C1 CDL G 301 " pdb=" CA2 CDL G 301 " ideal model delta sigma weight residual 113.28 104.83 8.45 3.06e+00 1.07e-01 7.60e+00 angle pdb=" CB2 CDL E 301 " pdb=" C1 CDL E 301 " pdb=" CA2 CDL E 301 " ideal model delta sigma weight residual 113.28 104.84 8.44 3.06e+00 1.07e-01 7.60e+00 angle pdb=" CB2 CDL A 301 " pdb=" C1 CDL A 301 " pdb=" CA2 CDL A 301 " ideal model delta sigma weight residual 113.28 104.84 8.44 3.06e+00 1.07e-01 7.60e+00 angle pdb=" CB2 CDL M 301 " pdb=" C1 CDL M 301 " pdb=" CA2 CDL M 301 " ideal model delta sigma weight residual 113.28 104.84 8.44 3.06e+00 1.07e-01 7.60e+00 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.13: 12706 29.13 - 58.27: 759 58.27 - 87.40: 31 87.40 - 116.54: 0 116.54 - 145.67: 8 Dihedral angle restraints: 13504 sinusoidal: 5424 harmonic: 8080 Sorted by residual: dihedral pdb=" CA5 CDL C 301 " pdb=" CA4 CDL C 301 " pdb=" OA6 CDL C 301 " pdb=" CA6 CDL C 301 " ideal model delta sinusoidal sigma weight residual 168.24 -46.09 -145.67 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA5 CDL G 301 " pdb=" CA4 CDL G 301 " pdb=" OA6 CDL G 301 " pdb=" CA6 CDL G 301 " ideal model delta sinusoidal sigma weight residual 168.24 -46.09 -145.67 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA5 CDL E 301 " pdb=" CA4 CDL E 301 " pdb=" OA6 CDL E 301 " pdb=" CA6 CDL E 301 " ideal model delta sinusoidal sigma weight residual 168.24 -46.10 -145.66 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 13501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3169 0.067 - 0.135: 263 0.135 - 0.202: 0 0.202 - 0.269: 0 0.269 - 0.336: 16 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CB4 CDL G 301 " pdb=" CB3 CDL G 301 " pdb=" CB6 CDL G 301 " pdb=" OB6 CDL G 301 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB4 CDL O 301 " pdb=" CB3 CDL O 301 " pdb=" CB6 CDL O 301 " pdb=" OB6 CDL O 301 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB4 CDL E 301 " pdb=" CB3 CDL E 301 " pdb=" CB6 CDL E 301 " pdb=" OB6 CDL E 301 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 3445 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 88 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C GLN C 88 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN C 88 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 89 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN O 88 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLN O 88 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN O 88 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL O 89 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN M 88 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C GLN M 88 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN M 88 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL M 89 " 0.010 2.00e-02 2.50e+03 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 148 2.60 - 3.18: 19521 3.18 - 3.75: 34940 3.75 - 4.33: 52004 4.33 - 4.90: 84810 Nonbonded interactions: 191423 Sorted by model distance: nonbonded pdb=" N GLN P 15 " pdb=" OE1 GLN P 15 " model vdw 2.025 3.120 nonbonded pdb=" N GLN F 15 " pdb=" OE1 GLN F 15 " model vdw 2.026 3.120 nonbonded pdb=" N GLN D 15 " pdb=" OE1 GLN D 15 " model vdw 2.026 3.120 nonbonded pdb=" N GLN L 15 " pdb=" OE1 GLN L 15 " model vdw 2.026 3.120 nonbonded pdb=" N GLN B 15 " pdb=" OE1 GLN B 15 " model vdw 2.026 3.120 ... (remaining 191418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.700 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 23120 Z= 0.133 Angle : 0.533 8.477 31232 Z= 0.284 Chirality : 0.042 0.336 3448 Planarity : 0.004 0.019 3912 Dihedral : 17.149 145.669 8392 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.59 % Favored : 96.13 % Rotamer: Outliers : 1.00 % Allowed : 15.78 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2896 helix: 1.02 (0.14), residues: 1432 sheet: 0.67 (0.24), residues: 480 loop : 0.04 (0.22), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 49 TYR 0.009 0.001 TYR G 223 PHE 0.010 0.001 PHE A 208 TRP 0.010 0.001 TRP I 14 HIS 0.002 0.001 HIS P 101 Details of bonding type rmsd covalent geometry : bond 0.00265 (23112) covalent geometry : angle 0.53257 (31216) SS BOND : bond 0.00020 ( 8) SS BOND : angle 0.44003 ( 16) hydrogen bonds : bond 0.10979 ( 1433) hydrogen bonds : angle 7.08282 ( 4107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 520 time to evaluate : 0.881 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 534 average time/residue: 0.8374 time to fit residues: 496.0164 Evaluate side-chains 526 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 504 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain M residue 137 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN B 80 ASN D 69 GLN D 80 ASN F 69 GLN F 80 ASN H 69 GLN H 80 ASN J 69 GLN J 80 ASN L 69 GLN L 80 ASN N 69 GLN N 80 ASN P 69 GLN P 80 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.064237 restraints weight = 28919.908| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 1.86 r_work: 0.2581 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 23120 Z= 0.128 Angle : 0.527 4.660 31232 Z= 0.285 Chirality : 0.039 0.119 3448 Planarity : 0.004 0.036 3912 Dihedral : 14.092 150.071 3918 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.46 % Allowed : 14.37 % Favored : 84.17 % 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: 1.85 (0.16), residues: 2896 helix: 2.33 (0.14), residues: 1448 sheet: 0.98 (0.25), residues: 448 loop : -0.29 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 49 TYR 0.010 0.001 TYR O 223 PHE 0.010 0.001 PHE G 207 TRP 0.010 0.001 TRP A 14 HIS 0.002 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00261 (23112) covalent geometry : angle 0.52685 (31216) SS BOND : bond 0.00016 ( 8) SS BOND : angle 0.44240 ( 16) hydrogen bonds : bond 0.05081 ( 1433) hydrogen bonds : angle 5.14421 ( 4107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 505 time to evaluate : 0.931 Fit side-chains REVERT: B 21 ARG cc_start: 0.8989 (ttt90) cc_final: 0.8660 (ttt-90) REVERT: B 49 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.6254 (mmt-90) REVERT: B 58 GLU cc_start: 0.9104 (pm20) cc_final: 0.8854 (pm20) REVERT: B 89 ASN cc_start: 0.8710 (t0) cc_final: 0.8485 (t0) REVERT: D 21 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8671 (ttt-90) REVERT: D 49 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.6259 (mmt-90) REVERT: D 58 GLU cc_start: 0.9106 (pm20) cc_final: 0.8853 (pm20) REVERT: D 89 ASN cc_start: 0.8717 (t0) cc_final: 0.8496 (t0) REVERT: D 104 GLU cc_start: 0.9342 (tt0) cc_final: 0.9075 (tt0) REVERT: F 21 ARG cc_start: 0.8989 (ttt90) cc_final: 0.8663 (ttt-90) REVERT: F 49 ARG cc_start: 0.7751 (mmt-90) cc_final: 0.6251 (mmt-90) REVERT: F 58 GLU cc_start: 0.9107 (pm20) cc_final: 0.8859 (pm20) REVERT: F 89 ASN cc_start: 0.8713 (t0) cc_final: 0.8491 (t0) REVERT: F 104 GLU cc_start: 0.9341 (tt0) cc_final: 0.9072 (tt0) REVERT: H 21 ARG cc_start: 0.9000 (ttt90) cc_final: 0.8677 (ttt-90) REVERT: H 49 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.6248 (mmt-90) REVERT: H 58 GLU cc_start: 0.9098 (pm20) cc_final: 0.8852 (pm20) REVERT: H 89 ASN cc_start: 0.8702 (t0) cc_final: 0.8471 (t0) REVERT: J 21 ARG cc_start: 0.8989 (ttt90) cc_final: 0.8662 (ttt-90) REVERT: J 58 GLU cc_start: 0.9104 (pm20) cc_final: 0.8858 (pm20) REVERT: J 89 ASN cc_start: 0.8709 (t0) cc_final: 0.8487 (t0) REVERT: J 104 GLU cc_start: 0.9343 (tt0) cc_final: 0.9075 (tt0) REVERT: L 21 ARG cc_start: 0.8984 (ttt90) cc_final: 0.8662 (ttt-90) REVERT: L 58 GLU cc_start: 0.9103 (pm20) cc_final: 0.8859 (pm20) REVERT: L 89 ASN cc_start: 0.8713 (t0) cc_final: 0.8490 (t0) REVERT: L 104 GLU cc_start: 0.9340 (tt0) cc_final: 0.9069 (tt0) REVERT: N 21 ARG cc_start: 0.8983 (ttt90) cc_final: 0.8659 (ttt-90) REVERT: N 58 GLU cc_start: 0.9097 (pm20) cc_final: 0.8844 (pm20) REVERT: N 89 ASN cc_start: 0.8702 (t0) cc_final: 0.8476 (t0) REVERT: P 21 ARG cc_start: 0.8984 (ttt90) cc_final: 0.8661 (ttt-90) REVERT: P 58 GLU cc_start: 0.9104 (pm20) cc_final: 0.8854 (pm20) REVERT: P 89 ASN cc_start: 0.8706 (t0) cc_final: 0.8483 (t0) outliers start: 32 outliers final: 8 residues processed: 513 average time/residue: 0.8715 time to fit residues: 495.3943 Evaluate side-chains 495 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 487 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain P residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 25 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 244 optimal weight: 0.0570 chunk 263 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN D 80 ASN F 80 ASN H 80 ASN J 80 ASN L 80 ASN N 80 ASN P 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.061738 restraints weight = 29021.382| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 1.84 r_work: 0.2526 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23120 Z= 0.190 Angle : 0.563 6.590 31232 Z= 0.306 Chirality : 0.042 0.121 3448 Planarity : 0.004 0.025 3912 Dihedral : 14.036 150.854 3896 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.55 % Allowed : 14.87 % Favored : 83.58 % 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: 1.78 (0.16), residues: 2896 helix: 2.31 (0.13), residues: 1448 sheet: 0.96 (0.25), residues: 448 loop : -0.41 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 49 TYR 0.011 0.001 TYR L 42 PHE 0.012 0.001 PHE O 208 TRP 0.014 0.002 TRP E 14 HIS 0.003 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00444 (23112) covalent geometry : angle 0.56344 (31216) SS BOND : bond 0.00037 ( 8) SS BOND : angle 0.57265 ( 16) hydrogen bonds : bond 0.06324 ( 1433) hydrogen bonds : angle 5.28118 ( 4107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 506 time to evaluate : 0.912 Fit side-chains REVERT: B 49 ARG cc_start: 0.7917 (mmt-90) cc_final: 0.6389 (mmt-90) REVERT: B 58 GLU cc_start: 0.9114 (pm20) cc_final: 0.8805 (pm20) REVERT: B 77 ASP cc_start: 0.8405 (t0) cc_final: 0.8018 (t0) REVERT: B 80 ASN cc_start: 0.9106 (m-40) cc_final: 0.8855 (m110) REVERT: B 89 ASN cc_start: 0.8769 (t0) cc_final: 0.8489 (t0) REVERT: D 49 ARG cc_start: 0.7915 (mmt-90) cc_final: 0.6390 (mmt-90) REVERT: D 58 GLU cc_start: 0.9111 (pm20) cc_final: 0.8800 (pm20) REVERT: D 77 ASP cc_start: 0.8423 (t0) cc_final: 0.8037 (t0) REVERT: D 80 ASN cc_start: 0.9109 (m-40) cc_final: 0.8858 (m110) REVERT: D 89 ASN cc_start: 0.8807 (t0) cc_final: 0.8534 (t0) REVERT: F 49 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.6389 (mmt-90) REVERT: F 58 GLU cc_start: 0.9111 (pm20) cc_final: 0.8803 (pm20) REVERT: F 77 ASP cc_start: 0.8418 (t0) cc_final: 0.8033 (t0) REVERT: F 80 ASN cc_start: 0.9109 (m-40) cc_final: 0.8856 (m110) REVERT: F 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8520 (t0) REVERT: H 49 ARG cc_start: 0.7912 (mmt-90) cc_final: 0.6380 (mmt-90) REVERT: H 77 ASP cc_start: 0.8403 (t0) cc_final: 0.8015 (t0) REVERT: H 80 ASN cc_start: 0.9107 (m-40) cc_final: 0.8856 (m110) REVERT: H 89 ASN cc_start: 0.8763 (t0) cc_final: 0.8482 (t0) REVERT: J 58 GLU cc_start: 0.9111 (pm20) cc_final: 0.8801 (pm20) REVERT: J 77 ASP cc_start: 0.8412 (t0) cc_final: 0.8027 (t0) REVERT: J 80 ASN cc_start: 0.9107 (m-40) cc_final: 0.8855 (m110) REVERT: J 89 ASN cc_start: 0.8803 (t0) cc_final: 0.8529 (t0) REVERT: L 77 ASP cc_start: 0.8413 (t0) cc_final: 0.8028 (t0) REVERT: L 80 ASN cc_start: 0.9106 (m-40) cc_final: 0.8856 (m110) REVERT: L 89 ASN cc_start: 0.8800 (t0) cc_final: 0.8526 (t0) REVERT: N 58 GLU cc_start: 0.9104 (pm20) cc_final: 0.8793 (pm20) REVERT: N 77 ASP cc_start: 0.8405 (t0) cc_final: 0.8019 (t0) REVERT: N 80 ASN cc_start: 0.9102 (m-40) cc_final: 0.8854 (m110) REVERT: N 89 ASN cc_start: 0.8764 (t0) cc_final: 0.8484 (t0) REVERT: P 58 GLU cc_start: 0.9109 (pm20) cc_final: 0.8799 (pm20) REVERT: P 77 ASP cc_start: 0.8405 (t0) cc_final: 0.8017 (t0) REVERT: P 80 ASN cc_start: 0.9101 (m-40) cc_final: 0.8850 (m110) REVERT: P 89 ASN cc_start: 0.8763 (t0) cc_final: 0.8483 (t0) outliers start: 34 outliers final: 18 residues processed: 516 average time/residue: 0.8245 time to fit residues: 474.7978 Evaluate side-chains 514 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 496 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 260 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 84 optimal weight: 0.0470 chunk 264 optimal weight: 0.0770 chunk 267 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.096585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.066857 restraints weight = 28908.332| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.85 r_work: 0.2636 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23120 Z= 0.102 Angle : 0.497 7.175 31232 Z= 0.264 Chirality : 0.038 0.121 3448 Planarity : 0.004 0.028 3912 Dihedral : 13.349 151.748 3896 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.93 % Favored : 97.79 % Rotamer: Outliers : 1.19 % Allowed : 14.19 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.16), residues: 2896 helix: 2.60 (0.14), residues: 1448 sheet: 0.93 (0.25), residues: 448 loop : -0.33 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 49 TYR 0.008 0.001 TYR C 223 PHE 0.010 0.001 PHE K 196 TRP 0.008 0.001 TRP A 14 HIS 0.001 0.000 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00196 (23112) covalent geometry : angle 0.49729 (31216) SS BOND : bond 0.00051 ( 8) SS BOND : angle 0.28133 ( 16) hydrogen bonds : bond 0.04041 ( 1433) hydrogen bonds : angle 4.87976 ( 4107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 519 time to evaluate : 0.779 Fit side-chains REVERT: B 21 ARG cc_start: 0.8971 (ttt90) cc_final: 0.8616 (ttt-90) REVERT: B 49 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.6305 (mmt-90) REVERT: B 58 GLU cc_start: 0.9184 (pm20) cc_final: 0.8830 (pm20) REVERT: B 89 ASN cc_start: 0.8799 (t0) cc_final: 0.8470 (t0) REVERT: B 104 GLU cc_start: 0.9355 (tt0) cc_final: 0.9118 (tt0) REVERT: D 21 ARG cc_start: 0.8983 (ttt90) cc_final: 0.8618 (ttt-90) REVERT: D 49 ARG cc_start: 0.7834 (mmt-90) cc_final: 0.6318 (mmt-90) REVERT: D 58 GLU cc_start: 0.9186 (pm20) cc_final: 0.8830 (pm20) REVERT: D 89 ASN cc_start: 0.8819 (t0) cc_final: 0.8485 (t0) REVERT: F 21 ARG cc_start: 0.8985 (ttt90) cc_final: 0.8620 (ttt-90) REVERT: F 49 ARG cc_start: 0.7833 (mmt-90) cc_final: 0.6313 (mmt-90) REVERT: F 58 GLU cc_start: 0.9189 (pm20) cc_final: 0.8835 (pm20) REVERT: F 89 ASN cc_start: 0.8814 (t0) cc_final: 0.8483 (t0) REVERT: H 21 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8617 (ttt-90) REVERT: H 49 ARG cc_start: 0.7824 (mmt-90) cc_final: 0.6301 (mmt-90) REVERT: H 58 GLU cc_start: 0.9184 (pm20) cc_final: 0.8831 (pm20) REVERT: H 89 ASN cc_start: 0.8791 (t0) cc_final: 0.8461 (t0) REVERT: J 21 ARG cc_start: 0.8998 (ttt90) cc_final: 0.8623 (ttt-90) REVERT: J 58 GLU cc_start: 0.9186 (pm20) cc_final: 0.8833 (pm20) REVERT: J 89 ASN cc_start: 0.8815 (t0) cc_final: 0.8481 (t0) REVERT: L 21 ARG cc_start: 0.8995 (ttt90) cc_final: 0.8620 (ttt-90) REVERT: L 58 GLU cc_start: 0.9190 (pm20) cc_final: 0.8840 (pm20) REVERT: L 89 ASN cc_start: 0.8818 (t0) cc_final: 0.8484 (t0) REVERT: N 21 ARG cc_start: 0.8983 (ttt90) cc_final: 0.8629 (ttt-90) REVERT: N 58 GLU cc_start: 0.9182 (pm20) cc_final: 0.8826 (pm20) REVERT: N 89 ASN cc_start: 0.8788 (t0) cc_final: 0.8459 (t0) REVERT: N 104 GLU cc_start: 0.9357 (tt0) cc_final: 0.9111 (tt0) REVERT: P 21 ARG cc_start: 0.8983 (ttt90) cc_final: 0.8611 (ttt-90) REVERT: P 58 GLU cc_start: 0.9183 (pm20) cc_final: 0.8826 (pm20) REVERT: P 89 ASN cc_start: 0.8795 (t0) cc_final: 0.8468 (t0) outliers start: 26 outliers final: 10 residues processed: 529 average time/residue: 0.8384 time to fit residues: 494.2990 Evaluate side-chains 504 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 494 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 283 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 188 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 80 ASN D 5 GLN D 80 ASN F 5 GLN F 80 ASN H 5 GLN H 80 ASN J 5 GLN J 80 ASN L 5 GLN L 80 ASN N 5 GLN N 80 ASN P 5 GLN P 80 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.066267 restraints weight = 28777.032| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 1.85 r_work: 0.2622 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23120 Z= 0.107 Angle : 0.506 7.254 31232 Z= 0.268 Chirality : 0.038 0.119 3448 Planarity : 0.003 0.026 3912 Dihedral : 13.125 151.750 3896 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.80 % Favored : 97.93 % Rotamer: Outliers : 1.19 % Allowed : 14.87 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.16), residues: 2896 helix: 2.65 (0.14), residues: 1448 sheet: 0.89 (0.25), residues: 448 loop : -0.28 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 49 TYR 0.009 0.001 TYR G 223 PHE 0.010 0.001 PHE C 196 TRP 0.008 0.001 TRP O 14 HIS 0.002 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00215 (23112) covalent geometry : angle 0.50643 (31216) SS BOND : bond 0.00030 ( 8) SS BOND : angle 0.36170 ( 16) hydrogen bonds : bond 0.04294 ( 1433) hydrogen bonds : angle 4.86594 ( 4107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 502 time to evaluate : 0.923 Fit side-chains REVERT: B 21 ARG cc_start: 0.8990 (ttt90) cc_final: 0.8626 (ttt-90) REVERT: B 49 ARG cc_start: 0.7829 (mmt-90) cc_final: 0.6335 (mmt-90) REVERT: B 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8797 (pm20) REVERT: B 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8436 (t0) REVERT: D 21 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8648 (ttt-90) REVERT: D 49 ARG cc_start: 0.7833 (mmt-90) cc_final: 0.6350 (mmt-90) REVERT: D 58 GLU cc_start: 0.9167 (pm20) cc_final: 0.8796 (pm20) REVERT: D 89 ASN cc_start: 0.8817 (t0) cc_final: 0.8473 (t0) REVERT: F 21 ARG cc_start: 0.8989 (ttt90) cc_final: 0.8635 (ttt-90) REVERT: F 49 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.6335 (mmt-90) REVERT: F 58 GLU cc_start: 0.9170 (pm20) cc_final: 0.8803 (pm20) REVERT: F 89 ASN cc_start: 0.8818 (t0) cc_final: 0.8478 (t0) REVERT: H 21 ARG cc_start: 0.8997 (ttt90) cc_final: 0.8637 (ttt-90) REVERT: H 49 ARG cc_start: 0.7831 (mmt-90) cc_final: 0.6345 (mmt-90) REVERT: H 58 GLU cc_start: 0.9167 (pm20) cc_final: 0.8799 (pm20) REVERT: H 89 ASN cc_start: 0.8781 (t0) cc_final: 0.8435 (t0) REVERT: J 21 ARG cc_start: 0.9005 (ttt90) cc_final: 0.8652 (ttt-90) REVERT: J 58 GLU cc_start: 0.9169 (pm20) cc_final: 0.8800 (pm20) REVERT: J 89 ASN cc_start: 0.8815 (t0) cc_final: 0.8474 (t0) REVERT: L 21 ARG cc_start: 0.8994 (ttt90) cc_final: 0.8640 (ttt-90) REVERT: L 58 GLU cc_start: 0.9175 (pm20) cc_final: 0.8808 (pm20) REVERT: L 89 ASN cc_start: 0.8812 (t0) cc_final: 0.8467 (t0) REVERT: N 21 ARG cc_start: 0.9012 (ttt90) cc_final: 0.8648 (ttt-90) REVERT: N 58 GLU cc_start: 0.9166 (pm20) cc_final: 0.8794 (pm20) REVERT: N 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8440 (t0) REVERT: P 21 ARG cc_start: 0.8995 (ttt90) cc_final: 0.8635 (ttt-90) REVERT: P 58 GLU cc_start: 0.9167 (pm20) cc_final: 0.8793 (pm20) REVERT: P 89 ASN cc_start: 0.8799 (t0) cc_final: 0.8461 (t0) outliers start: 26 outliers final: 18 residues processed: 512 average time/residue: 0.8373 time to fit residues: 477.7780 Evaluate side-chains 511 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 493 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 101 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 69 GLN B 80 ASN D 5 GLN D 69 GLN D 80 ASN F 5 GLN F 69 GLN F 80 ASN H 5 GLN H 69 GLN H 80 ASN J 5 GLN J 69 GLN J 80 ASN L 5 GLN L 69 GLN L 80 ASN N 5 GLN N 69 GLN N 80 ASN P 5 GLN P 69 GLN P 80 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.061675 restraints weight = 29007.127| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 1.83 r_work: 0.2522 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 23120 Z= 0.210 Angle : 0.583 6.899 31232 Z= 0.315 Chirality : 0.043 0.119 3448 Planarity : 0.004 0.024 3912 Dihedral : 13.561 151.625 3896 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.28 % Allowed : 15.56 % Favored : 83.17 % 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: 1.77 (0.16), residues: 2896 helix: 2.32 (0.14), residues: 1448 sheet: 0.89 (0.25), residues: 448 loop : -0.40 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 238 TYR 0.011 0.002 TYR J 42 PHE 0.012 0.002 PHE K 208 TRP 0.014 0.002 TRP I 14 HIS 0.004 0.001 HIS K 124 Details of bonding type rmsd covalent geometry : bond 0.00497 (23112) covalent geometry : angle 0.58353 (31216) SS BOND : bond 0.00046 ( 8) SS BOND : angle 0.48037 ( 16) hydrogen bonds : bond 0.06417 ( 1433) hydrogen bonds : angle 5.25923 ( 4107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 505 time to evaluate : 1.011 Fit side-chains REVERT: B 49 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.6437 (mmt-90) REVERT: B 58 GLU cc_start: 0.9172 (pm20) cc_final: 0.8793 (pm20) REVERT: B 77 ASP cc_start: 0.8454 (t0) cc_final: 0.8092 (t0) REVERT: B 80 ASN cc_start: 0.9107 (m-40) cc_final: 0.8863 (m110) REVERT: B 89 ASN cc_start: 0.8774 (t0) cc_final: 0.8453 (t0) REVERT: B 104 GLU cc_start: 0.9319 (tt0) cc_final: 0.9107 (tt0) REVERT: D 49 ARG cc_start: 0.7984 (mmt-90) cc_final: 0.6447 (mmt-90) REVERT: D 58 GLU cc_start: 0.9171 (pm20) cc_final: 0.8794 (pm20) REVERT: D 77 ASP cc_start: 0.8467 (t0) cc_final: 0.8106 (t0) REVERT: D 80 ASN cc_start: 0.9113 (m-40) cc_final: 0.8866 (m110) REVERT: D 89 ASN cc_start: 0.8823 (t0) cc_final: 0.8502 (t0) REVERT: F 49 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.6425 (mmt-90) REVERT: F 58 GLU cc_start: 0.9173 (pm20) cc_final: 0.8798 (pm20) REVERT: F 77 ASP cc_start: 0.8459 (t0) cc_final: 0.8098 (t0) REVERT: F 80 ASN cc_start: 0.9111 (m-40) cc_final: 0.8866 (m110) REVERT: F 89 ASN cc_start: 0.8817 (t0) cc_final: 0.8478 (t0) REVERT: H 49 ARG cc_start: 0.7998 (mmt-90) cc_final: 0.6435 (mmt-90) REVERT: H 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8876 (pm20) REVERT: H 77 ASP cc_start: 0.8453 (t0) cc_final: 0.8073 (t0) REVERT: H 80 ASN cc_start: 0.9113 (m-40) cc_final: 0.8868 (m110) REVERT: H 89 ASN cc_start: 0.8779 (t0) cc_final: 0.8457 (t0) REVERT: H 104 GLU cc_start: 0.9330 (tt0) cc_final: 0.9122 (tt0) REVERT: J 58 GLU cc_start: 0.9173 (pm20) cc_final: 0.8795 (pm20) REVERT: J 77 ASP cc_start: 0.8459 (t0) cc_final: 0.8098 (t0) REVERT: J 80 ASN cc_start: 0.9110 (m-40) cc_final: 0.8862 (m110) REVERT: J 89 ASN cc_start: 0.8819 (t0) cc_final: 0.8481 (t0) REVERT: J 104 GLU cc_start: 0.9324 (tt0) cc_final: 0.9118 (tt0) REVERT: L 58 GLU cc_start: 0.9171 (pm20) cc_final: 0.8879 (pm20) REVERT: L 77 ASP cc_start: 0.8450 (t0) cc_final: 0.8088 (t0) REVERT: L 80 ASN cc_start: 0.9113 (m-40) cc_final: 0.8867 (m110) REVERT: L 89 ASN cc_start: 0.8812 (t0) cc_final: 0.8489 (t0) REVERT: L 104 GLU cc_start: 0.9322 (tt0) cc_final: 0.9113 (tt0) REVERT: N 58 GLU cc_start: 0.9171 (pm20) cc_final: 0.8793 (pm20) REVERT: N 77 ASP cc_start: 0.8442 (t0) cc_final: 0.8080 (t0) REVERT: N 80 ASN cc_start: 0.9099 (m-40) cc_final: 0.8869 (m110) REVERT: N 89 ASN cc_start: 0.8786 (t0) cc_final: 0.8469 (t0) REVERT: N 104 GLU cc_start: 0.9329 (tt0) cc_final: 0.9119 (tt0) REVERT: P 58 GLU cc_start: 0.9173 (pm20) cc_final: 0.8797 (pm20) REVERT: P 77 ASP cc_start: 0.8449 (t0) cc_final: 0.8068 (t0) REVERT: P 80 ASN cc_start: 0.9107 (m-40) cc_final: 0.8864 (m110) REVERT: P 89 ASN cc_start: 0.8780 (t0) cc_final: 0.8465 (t0) REVERT: P 104 GLU cc_start: 0.9325 (tt0) cc_final: 0.9114 (tt0) outliers start: 28 outliers final: 20 residues processed: 515 average time/residue: 0.7951 time to fit residues: 458.0153 Evaluate side-chains 517 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 497 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN D 5 GLN F 5 GLN H 5 GLN J 5 GLN L 5 GLN N 5 GLN P 5 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.062735 restraints weight = 28910.254| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 1.87 r_work: 0.2548 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23120 Z= 0.155 Angle : 0.558 6.441 31232 Z= 0.300 Chirality : 0.040 0.117 3448 Planarity : 0.004 0.025 3912 Dihedral : 13.275 152.118 3896 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.19 % Allowed : 14.83 % Favored : 83.99 % 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: 1.79 (0.16), residues: 2896 helix: 2.38 (0.14), residues: 1448 sheet: 0.85 (0.25), residues: 448 loop : -0.45 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 49 TYR 0.009 0.001 TYR K 223 PHE 0.011 0.001 PHE M 196 TRP 0.012 0.001 TRP I 14 HIS 0.002 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00353 (23112) covalent geometry : angle 0.55840 (31216) SS BOND : bond 0.00005 ( 8) SS BOND : angle 0.39252 ( 16) hydrogen bonds : bond 0.05536 ( 1433) hydrogen bonds : angle 5.16368 ( 4107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 505 time to evaluate : 0.756 Fit side-chains REVERT: B 49 ARG cc_start: 0.7969 (mmt-90) cc_final: 0.6432 (mmt-90) REVERT: B 58 GLU cc_start: 0.9165 (pm20) cc_final: 0.8791 (pm20) REVERT: B 77 ASP cc_start: 0.8460 (t0) cc_final: 0.8074 (t0) REVERT: B 80 ASN cc_start: 0.9095 (m-40) cc_final: 0.8833 (m110) REVERT: B 89 ASN cc_start: 0.8765 (t0) cc_final: 0.8433 (t0) REVERT: B 104 GLU cc_start: 0.9324 (tt0) cc_final: 0.9120 (tt0) REVERT: D 49 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.6455 (mmt-90) REVERT: D 58 GLU cc_start: 0.9153 (pm20) cc_final: 0.8776 (pm20) REVERT: D 77 ASP cc_start: 0.8465 (t0) cc_final: 0.8081 (t0) REVERT: D 80 ASN cc_start: 0.9085 (m-40) cc_final: 0.8830 (m110) REVERT: D 89 ASN cc_start: 0.8827 (t0) cc_final: 0.8498 (t0) REVERT: D 104 GLU cc_start: 0.9324 (tt0) cc_final: 0.9118 (tt0) REVERT: F 49 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.6438 (mmt-90) REVERT: F 58 GLU cc_start: 0.9164 (pm20) cc_final: 0.8791 (pm20) REVERT: F 77 ASP cc_start: 0.8466 (t0) cc_final: 0.8079 (t0) REVERT: F 80 ASN cc_start: 0.9087 (m-40) cc_final: 0.8822 (m110) REVERT: F 89 ASN cc_start: 0.8817 (t0) cc_final: 0.8471 (t0) REVERT: F 104 GLU cc_start: 0.9322 (tt0) cc_final: 0.9113 (tt0) REVERT: H 49 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.6431 (mmt-90) REVERT: H 58 GLU cc_start: 0.9175 (pm20) cc_final: 0.8807 (pm20) REVERT: H 77 ASP cc_start: 0.8451 (t0) cc_final: 0.8062 (t0) REVERT: H 80 ASN cc_start: 0.9089 (m-40) cc_final: 0.8829 (m110) REVERT: H 89 ASN cc_start: 0.8757 (t0) cc_final: 0.8425 (t0) REVERT: H 104 GLU cc_start: 0.9328 (tt0) cc_final: 0.9120 (tt0) REVERT: J 58 GLU cc_start: 0.9160 (pm20) cc_final: 0.8785 (pm20) REVERT: J 77 ASP cc_start: 0.8453 (t0) cc_final: 0.8068 (t0) REVERT: J 80 ASN cc_start: 0.9081 (m-40) cc_final: 0.8824 (m110) REVERT: J 89 ASN cc_start: 0.8816 (t0) cc_final: 0.8471 (t0) REVERT: J 104 GLU cc_start: 0.9326 (tt0) cc_final: 0.9123 (tt0) REVERT: L 58 GLU cc_start: 0.9179 (pm20) cc_final: 0.8814 (pm20) REVERT: L 77 ASP cc_start: 0.8450 (t0) cc_final: 0.8065 (t0) REVERT: L 80 ASN cc_start: 0.9085 (m-40) cc_final: 0.8831 (m110) REVERT: L 89 ASN cc_start: 0.8823 (t0) cc_final: 0.8493 (t0) REVERT: L 104 GLU cc_start: 0.9322 (tt0) cc_final: 0.9115 (tt0) REVERT: N 58 GLU cc_start: 0.9155 (pm20) cc_final: 0.8777 (pm20) REVERT: N 77 ASP cc_start: 0.8426 (t0) cc_final: 0.8060 (t0) REVERT: N 80 ASN cc_start: 0.9078 (m-40) cc_final: 0.8815 (m110) REVERT: N 89 ASN cc_start: 0.8762 (t0) cc_final: 0.8422 (t0) REVERT: N 104 GLU cc_start: 0.9327 (tt0) cc_final: 0.9122 (tt0) REVERT: P 58 GLU cc_start: 0.9167 (pm20) cc_final: 0.8793 (pm20) REVERT: P 77 ASP cc_start: 0.8454 (t0) cc_final: 0.8065 (t0) REVERT: P 80 ASN cc_start: 0.9082 (m-40) cc_final: 0.8819 (m110) REVERT: P 89 ASN cc_start: 0.8754 (t0) cc_final: 0.8417 (t0) REVERT: P 104 GLU cc_start: 0.9323 (tt0) cc_final: 0.9113 (tt0) outliers start: 26 outliers final: 18 residues processed: 515 average time/residue: 0.7880 time to fit residues: 453.8240 Evaluate side-chains 515 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 497 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 280 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN D 5 GLN F 5 GLN H 5 GLN J 5 GLN L 5 GLN N 5 GLN P 5 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.094224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.063957 restraints weight = 28608.821| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 1.87 r_work: 0.2573 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23120 Z= 0.130 Angle : 0.542 6.436 31232 Z= 0.291 Chirality : 0.039 0.117 3448 Planarity : 0.004 0.026 3912 Dihedral : 13.036 152.327 3896 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.19 % Allowed : 14.74 % Favored : 84.08 % 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: 1.87 (0.16), residues: 2896 helix: 2.47 (0.14), residues: 1448 sheet: 0.81 (0.25), residues: 448 loop : -0.41 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 49 TYR 0.010 0.001 TYR E 223 PHE 0.011 0.001 PHE G 208 TRP 0.011 0.001 TRP E 14 HIS 0.002 0.001 HIS M 124 Details of bonding type rmsd covalent geometry : bond 0.00281 (23112) covalent geometry : angle 0.54193 (31216) SS BOND : bond 0.00004 ( 8) SS BOND : angle 0.35645 ( 16) hydrogen bonds : bond 0.04993 ( 1433) hydrogen bonds : angle 5.05921 ( 4107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 507 time to evaluate : 0.908 Fit side-chains REVERT: B 49 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.6499 (mmt-90) REVERT: B 58 GLU cc_start: 0.9165 (pm20) cc_final: 0.8810 (pm20) REVERT: B 77 ASP cc_start: 0.8421 (t0) cc_final: 0.8059 (t0) REVERT: B 80 ASN cc_start: 0.9037 (m-40) cc_final: 0.8789 (m110) REVERT: B 89 ASN cc_start: 0.8770 (t0) cc_final: 0.8414 (t0) REVERT: D 49 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.6517 (mmt-90) REVERT: D 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8805 (pm20) REVERT: D 77 ASP cc_start: 0.8428 (t0) cc_final: 0.8073 (t0) REVERT: D 80 ASN cc_start: 0.9036 (m-40) cc_final: 0.8804 (m110) REVERT: D 89 ASN cc_start: 0.8826 (t0) cc_final: 0.8496 (t0) REVERT: D 104 GLU cc_start: 0.9328 (tt0) cc_final: 0.9123 (tt0) REVERT: F 49 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.6501 (mmt-90) REVERT: F 58 GLU cc_start: 0.9170 (pm20) cc_final: 0.8781 (pm20) REVERT: F 77 ASP cc_start: 0.8428 (t0) cc_final: 0.8066 (t0) REVERT: F 80 ASN cc_start: 0.9041 (m-40) cc_final: 0.8793 (m110) REVERT: F 89 ASN cc_start: 0.8821 (t0) cc_final: 0.8478 (t0) REVERT: F 104 GLU cc_start: 0.9329 (tt0) cc_final: 0.9125 (tt0) REVERT: H 49 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.6500 (mmt-90) REVERT: H 58 GLU cc_start: 0.9161 (pm20) cc_final: 0.8807 (pm20) REVERT: H 77 ASP cc_start: 0.8417 (t0) cc_final: 0.8033 (t0) REVERT: H 80 ASN cc_start: 0.9031 (m-40) cc_final: 0.8787 (m110) REVERT: H 89 ASN cc_start: 0.8769 (t0) cc_final: 0.8415 (t0) REVERT: H 104 GLU cc_start: 0.9332 (tt0) cc_final: 0.9131 (tt0) REVERT: J 58 GLU cc_start: 0.9169 (pm20) cc_final: 0.8814 (pm20) REVERT: J 77 ASP cc_start: 0.8419 (t0) cc_final: 0.8063 (t0) REVERT: J 80 ASN cc_start: 0.9032 (m-40) cc_final: 0.8799 (m110) REVERT: J 89 ASN cc_start: 0.8822 (t0) cc_final: 0.8478 (t0) REVERT: J 104 GLU cc_start: 0.9329 (tt0) cc_final: 0.9125 (tt0) REVERT: L 58 GLU cc_start: 0.9169 (pm20) cc_final: 0.8818 (pm20) REVERT: L 77 ASP cc_start: 0.8415 (t0) cc_final: 0.8058 (t0) REVERT: L 80 ASN cc_start: 0.9035 (m-40) cc_final: 0.8804 (m110) REVERT: L 89 ASN cc_start: 0.8821 (t0) cc_final: 0.8489 (t0) REVERT: L 104 GLU cc_start: 0.9324 (tt0) cc_final: 0.9118 (tt0) REVERT: N 58 GLU cc_start: 0.9163 (pm20) cc_final: 0.8807 (pm20) REVERT: N 77 ASP cc_start: 0.8404 (t0) cc_final: 0.8038 (t0) REVERT: N 80 ASN cc_start: 0.9024 (m-40) cc_final: 0.8766 (m110) REVERT: N 89 ASN cc_start: 0.8767 (t0) cc_final: 0.8428 (t0) REVERT: P 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8812 (pm20) REVERT: P 77 ASP cc_start: 0.8421 (t0) cc_final: 0.8059 (t0) REVERT: P 80 ASN cc_start: 0.9030 (m-40) cc_final: 0.8781 (m110) REVERT: P 89 ASN cc_start: 0.8762 (t0) cc_final: 0.8425 (t0) REVERT: P 104 GLU cc_start: 0.9326 (tt0) cc_final: 0.9123 (tt0) outliers start: 26 outliers final: 18 residues processed: 517 average time/residue: 0.8036 time to fit residues: 464.0658 Evaluate side-chains 513 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 495 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 136 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 185 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN D 5 GLN F 5 GLN H 5 GLN J 5 GLN L 5 GLN N 5 GLN P 5 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.062048 restraints weight = 28914.715| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 1.87 r_work: 0.2534 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23120 Z= 0.180 Angle : 0.584 6.550 31232 Z= 0.316 Chirality : 0.041 0.117 3448 Planarity : 0.004 0.026 3912 Dihedral : 13.253 152.340 3896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.93 % Favored : 97.79 % Rotamer: Outliers : 1.19 % Allowed : 15.10 % Favored : 83.71 % 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: 1.74 (0.16), residues: 2896 helix: 2.34 (0.14), residues: 1448 sheet: 0.81 (0.25), residues: 448 loop : -0.47 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 49 TYR 0.010 0.001 TYR O 223 PHE 0.012 0.001 PHE G 208 TRP 0.013 0.001 TRP M 14 HIS 0.003 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00420 (23112) covalent geometry : angle 0.58441 (31216) SS BOND : bond 0.00006 ( 8) SS BOND : angle 0.41502 ( 16) hydrogen bonds : bond 0.05912 ( 1433) hydrogen bonds : angle 5.21867 ( 4107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 506 time to evaluate : 0.774 Fit side-chains REVERT: B 49 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.6459 (mmt-90) REVERT: B 58 GLU cc_start: 0.9159 (pm20) cc_final: 0.8751 (pm20) REVERT: B 77 ASP cc_start: 0.8444 (t0) cc_final: 0.8086 (t0) REVERT: B 80 ASN cc_start: 0.9055 (m-40) cc_final: 0.8817 (m110) REVERT: B 89 ASN cc_start: 0.8764 (t0) cc_final: 0.8442 (t0) REVERT: D 49 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.6483 (mmt-90) REVERT: D 58 GLU cc_start: 0.9157 (pm20) cc_final: 0.8746 (pm20) REVERT: D 77 ASP cc_start: 0.8456 (t0) cc_final: 0.8099 (t0) REVERT: D 80 ASN cc_start: 0.9056 (m-40) cc_final: 0.8815 (m110) REVERT: D 89 ASN cc_start: 0.8830 (t0) cc_final: 0.8502 (t0) REVERT: D 104 GLU cc_start: 0.9320 (tt0) cc_final: 0.9112 (tt0) REVERT: F 49 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.6553 (mmt-90) REVERT: F 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8752 (pm20) REVERT: F 77 ASP cc_start: 0.8456 (t0) cc_final: 0.8100 (t0) REVERT: F 80 ASN cc_start: 0.9062 (m-40) cc_final: 0.8827 (m110) REVERT: F 89 ASN cc_start: 0.8828 (t0) cc_final: 0.8485 (t0) REVERT: F 104 GLU cc_start: 0.9318 (tt0) cc_final: 0.9106 (tt0) REVERT: H 49 ARG cc_start: 0.8018 (mmt-90) cc_final: 0.6464 (mmt-90) REVERT: H 58 GLU cc_start: 0.9154 (pm20) cc_final: 0.8774 (pm20) REVERT: H 77 ASP cc_start: 0.8441 (t0) cc_final: 0.8085 (t0) REVERT: H 80 ASN cc_start: 0.9053 (m-40) cc_final: 0.8817 (m110) REVERT: H 89 ASN cc_start: 0.8756 (t0) cc_final: 0.8437 (t0) REVERT: H 104 GLU cc_start: 0.9325 (tt0) cc_final: 0.9119 (tt0) REVERT: J 58 GLU cc_start: 0.9158 (pm20) cc_final: 0.8749 (pm20) REVERT: J 77 ASP cc_start: 0.8440 (t0) cc_final: 0.8083 (t0) REVERT: J 80 ASN cc_start: 0.9055 (m-40) cc_final: 0.8814 (m110) REVERT: J 89 ASN cc_start: 0.8834 (t0) cc_final: 0.8491 (t0) REVERT: J 104 GLU cc_start: 0.9322 (tt0) cc_final: 0.9113 (tt0) REVERT: L 58 GLU cc_start: 0.9159 (pm20) cc_final: 0.8782 (pm20) REVERT: L 77 ASP cc_start: 0.8437 (t0) cc_final: 0.8079 (t0) REVERT: L 80 ASN cc_start: 0.9056 (m-40) cc_final: 0.8818 (m110) REVERT: L 89 ASN cc_start: 0.8821 (t0) cc_final: 0.8491 (t0) REVERT: L 104 GLU cc_start: 0.9318 (tt0) cc_final: 0.9108 (tt0) REVERT: N 58 GLU cc_start: 0.9156 (pm20) cc_final: 0.8745 (pm20) REVERT: N 77 ASP cc_start: 0.8440 (t0) cc_final: 0.8084 (t0) REVERT: N 80 ASN cc_start: 0.9059 (m-40) cc_final: 0.8825 (m110) REVERT: N 89 ASN cc_start: 0.8755 (t0) cc_final: 0.8439 (t0) REVERT: P 58 GLU cc_start: 0.9161 (pm20) cc_final: 0.8752 (pm20) REVERT: P 77 ASP cc_start: 0.8443 (t0) cc_final: 0.8085 (t0) REVERT: P 80 ASN cc_start: 0.9058 (m-40) cc_final: 0.8821 (m110) REVERT: P 89 ASN cc_start: 0.8755 (t0) cc_final: 0.8440 (t0) REVERT: P 104 GLU cc_start: 0.9318 (tt0) cc_final: 0.9109 (tt0) outliers start: 26 outliers final: 26 residues processed: 516 average time/residue: 0.7101 time to fit residues: 410.2198 Evaluate side-chains 524 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 498 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain K residue 50 MET Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 57 optimal weight: 0.0060 chunk 218 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN D 5 GLN F 5 GLN H 5 GLN J 5 GLN L 5 GLN N 5 GLN P 5 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.066359 restraints weight = 28743.858| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 1.86 r_work: 0.2626 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23120 Z= 0.109 Angle : 0.533 6.554 31232 Z= 0.285 Chirality : 0.038 0.122 3448 Planarity : 0.004 0.027 3912 Dihedral : 12.753 152.670 3896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.07 % Favored : 97.65 % Rotamer: Outliers : 0.82 % Allowed : 15.42 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.01 (0.16), residues: 2896 helix: 2.62 (0.14), residues: 1448 sheet: 0.83 (0.25), residues: 448 loop : -0.39 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 49 TYR 0.008 0.001 TYR C 223 PHE 0.009 0.001 PHE M 196 TRP 0.009 0.001 TRP A 14 HIS 0.002 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00221 (23112) covalent geometry : angle 0.53339 (31216) SS BOND : bond 0.00028 ( 8) SS BOND : angle 0.32470 ( 16) hydrogen bonds : bond 0.04126 ( 1433) hydrogen bonds : angle 4.91144 ( 4107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 529 time to evaluate : 0.918 Fit side-chains REVERT: B 49 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.6490 (mmt-90) REVERT: B 58 GLU cc_start: 0.9163 (pm20) cc_final: 0.8778 (pm20) REVERT: B 89 ASN cc_start: 0.8783 (t0) cc_final: 0.8440 (t0) REVERT: D 49 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.6511 (mmt-90) REVERT: D 58 GLU cc_start: 0.9160 (pm20) cc_final: 0.8773 (pm20) REVERT: D 89 ASN cc_start: 0.8826 (t0) cc_final: 0.8472 (t0) REVERT: F 49 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.6493 (mmt-90) REVERT: F 58 GLU cc_start: 0.9165 (pm20) cc_final: 0.8783 (pm20) REVERT: F 77 ASP cc_start: 0.8408 (t0) cc_final: 0.8026 (t0) REVERT: F 80 ASN cc_start: 0.9054 (m-40) cc_final: 0.8790 (m110) REVERT: F 89 ASN cc_start: 0.8826 (t0) cc_final: 0.8473 (t0) REVERT: F 104 GLU cc_start: 0.9342 (tt0) cc_final: 0.9138 (tt0) REVERT: H 49 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.6494 (mmt-90) REVERT: H 58 GLU cc_start: 0.9159 (pm20) cc_final: 0.8777 (pm20) REVERT: H 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8447 (t0) REVERT: H 104 GLU cc_start: 0.9346 (tt0) cc_final: 0.9143 (tt0) REVERT: J 58 GLU cc_start: 0.9163 (pm20) cc_final: 0.8779 (pm20) REVERT: J 77 ASP cc_start: 0.8403 (t0) cc_final: 0.8020 (t0) REVERT: J 80 ASN cc_start: 0.9057 (m-40) cc_final: 0.8785 (m110) REVERT: J 89 ASN cc_start: 0.8821 (t0) cc_final: 0.8467 (t0) REVERT: J 104 GLU cc_start: 0.9347 (tt0) cc_final: 0.9097 (tt0) REVERT: L 58 GLU cc_start: 0.9163 (pm20) cc_final: 0.8781 (pm20) REVERT: L 89 ASN cc_start: 0.8819 (t0) cc_final: 0.8465 (t0) REVERT: N 58 GLU cc_start: 0.9159 (pm20) cc_final: 0.8772 (pm20) REVERT: N 89 ASN cc_start: 0.8781 (t0) cc_final: 0.8443 (t0) REVERT: P 58 GLU cc_start: 0.9165 (pm20) cc_final: 0.8777 (pm20) REVERT: P 89 ASN cc_start: 0.8786 (t0) cc_final: 0.8453 (t0) REVERT: P 104 GLU cc_start: 0.9339 (tt0) cc_final: 0.9135 (tt0) outliers start: 18 outliers final: 18 residues processed: 539 average time/residue: 0.8243 time to fit residues: 495.8578 Evaluate side-chains 526 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 508 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 177 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 250 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 80 ASN D 5 GLN D 80 ASN F 5 GLN H 5 GLN H 80 ASN J 5 GLN L 5 GLN L 80 ASN N 5 GLN N 80 ASN P 5 GLN P 80 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.092183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.061718 restraints weight = 28891.299| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 1.87 r_work: 0.2524 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23120 Z= 0.191 Angle : 0.598 7.052 31232 Z= 0.324 Chirality : 0.042 0.119 3448 Planarity : 0.004 0.027 3912 Dihedral : 13.194 152.297 3896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 0.82 % Allowed : 15.69 % Favored : 83.49 % 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 (0.16), residues: 2896 helix: 2.34 (0.14), residues: 1448 sheet: 0.79 (0.25), residues: 448 loop : -0.47 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 238 TYR 0.010 0.002 TYR O 223 PHE 0.012 0.001 PHE I 196 TRP 0.013 0.001 TRP O 14 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00448 (23112) covalent geometry : angle 0.59837 (31216) SS BOND : bond 0.00025 ( 8) SS BOND : angle 0.41781 ( 16) hydrogen bonds : bond 0.06196 ( 1433) hydrogen bonds : angle 5.25578 ( 4107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14052.06 seconds wall clock time: 238 minutes 40.69 seconds (14320.69 seconds total)