Starting phenix.real_space_refine on Sat Jul 4 21:23:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy6_42793/07_2026/8uy6_42793_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy6_42793/07_2026/8uy6_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_42793/07_2026/8uy6_42793_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy6_42793/07_2026/8uy6_42793_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uy6_42793/07_2026/8uy6_42793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy6_42793/07_2026/8uy6_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-dev-6108/lib/python3.11/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: 4.29, per 1000 atoms: 0.19 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: 1.59 Conformation dependent library (CDL) restraints added in 934.7 milliseconds 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: 0.69 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: 4.02 Time building geometry restraints manager: 2.14 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=" OB5 CDL I 301 " pdb=" PB2 CDL I 301 " ideal model delta sigma weight residual 1.657 1.579 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" OB5 CDL A 301 " pdb=" PB2 CDL A 301 " ideal model delta sigma weight residual 1.657 1.579 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" OB5 CDL C 301 " pdb=" PB2 CDL C 301 " ideal model delta sigma weight residual 1.657 1.579 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" OB5 CDL K 301 " pdb=" PB2 CDL K 301 " ideal model delta sigma weight residual 1.657 1.579 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" OB5 CDL M 301 " pdb=" PB2 CDL M 301 " ideal model delta sigma weight residual 1.657 1.579 0.078 2.00e-02 2.50e+03 1.50e+01 ... (remaining 23107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 30315 1.48 - 2.95: 701 2.95 - 4.43: 104 4.43 - 5.90: 32 5.90 - 7.38: 64 Bond angle restraints: 31216 Sorted by residual: angle pdb=" OA3 CDL M 301 " pdb=" PA1 CDL M 301 " pdb=" OA4 CDL M 301 " ideal model delta sigma weight residual 121.92 114.54 7.38 3.00e+00 1.11e-01 6.05e+00 angle pdb=" OA3 CDL I 301 " pdb=" PA1 CDL I 301 " pdb=" OA4 CDL I 301 " ideal model delta sigma weight residual 121.92 114.54 7.38 3.00e+00 1.11e-01 6.05e+00 angle pdb=" OA3 CDL G 301 " pdb=" PA1 CDL G 301 " pdb=" OA4 CDL G 301 " ideal model delta sigma weight residual 121.92 114.54 7.38 3.00e+00 1.11e-01 6.05e+00 angle pdb=" OA3 CDL C 301 " pdb=" PA1 CDL C 301 " pdb=" OA4 CDL C 301 " ideal model delta sigma weight residual 121.92 114.54 7.38 3.00e+00 1.11e-01 6.05e+00 angle pdb=" OA3 CDL A 301 " pdb=" PA1 CDL A 301 " pdb=" OA4 CDL A 301 " ideal model delta sigma weight residual 121.92 114.54 7.38 3.00e+00 1.11e-01 6.05e+00 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 11303 15.28 - 30.55: 1526 30.55 - 45.83: 565 45.83 - 61.10: 208 61.10 - 76.38: 30 Dihedral angle restraints: 13632 sinusoidal: 5552 harmonic: 8080 Sorted by residual: dihedral pdb=" CA ILE E 176 " pdb=" C ILE E 176 " pdb=" N SER E 177 " pdb=" CA SER E 177 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE C 176 " pdb=" C ILE C 176 " pdb=" N SER C 177 " pdb=" CA SER C 177 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE O 176 " pdb=" C ILE O 176 " pdb=" N SER O 177 " pdb=" CA SER O 177 " ideal model delta harmonic sigma weight residual -180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 13629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3160 0.066 - 0.132: 272 0.132 - 0.198: 0 0.198 - 0.264: 0 0.264 - 0.330: 16 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CA4 CDL A 301 " pdb=" CA3 CDL A 301 " pdb=" CA6 CDL A 301 " pdb=" OA6 CDL A 301 " both_signs ideal model delta sigma weight residual False -2.53 -2.86 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA4 CDL M 301 " pdb=" CA3 CDL M 301 " pdb=" CA6 CDL M 301 " pdb=" OA6 CDL M 301 " both_signs ideal model delta sigma weight residual False -2.53 -2.86 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA4 CDL C 301 " pdb=" CA3 CDL C 301 " pdb=" CA6 CDL C 301 " pdb=" OA6 CDL C 301 " both_signs ideal model delta sigma weight residual False -2.53 -2.86 0.33 2.00e-01 2.50e+01 2.72e+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: 0.09 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.390 Find NCS groups from input model: 0.230 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9347 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 : 0.004 0.078 23120 Z= 0.222 Angle : 0.616 7.381 31232 Z= 0.297 Chirality : 0.042 0.330 3448 Planarity : 0.004 0.019 3912 Dihedral : 17.185 76.377 8520 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 are 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/Z covalent geometry : bond 0.00442 / 0.22 (23112) covalent geometry : angle 0.61629 / 0.30 (31216) SS BOND : bond 0.00020 / 0.01 ( 8) SS BOND : angle 0.44003 / 0.26 ( 16) hydrogen bonds : bond 0.10979 / 7.39 ( 1433) hydrogen bonds : angle 7.08282 / 5.17 ( 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 : 0.808 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 534 average time/residue: 0.7235 time to fit residues: 429.9428 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 : 0.722 ------------------------------------------------------------------------------- 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: 0.9980 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: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3275 r_free = 0.3275 target = 0.094003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.064087 restraints weight = 28877.328| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 1.86 r_work: 0.2579 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9282 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 23120 Z= 0.127 Angle : 0.532 4.663 31232 Z= 0.284 Chirality : 0.039 0.120 3448 Planarity : 0.004 0.036 3912 Dihedral : 12.503 62.912 4046 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.86 % Favored : 97.86 % Rotamer: Outliers : 1.14 % Allowed : 14.37 % Favored : 84.49 % 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 are not related in a simple way. whole: 1.84 (0.16), residues: 2896 helix: 2.31 (0.14), residues: 1448 sheet: 0.97 (0.25), residues: 448 loop : -0.28 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 49 TYR 0.009 0.001 TYR O 223 PHE 0.009 0.001 PHE E 207 TRP 0.010 0.001 TRP E 14 HIS 0.002 0.001 HIS I 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (23112) covalent geometry : angle 0.53154 / 0.28 (31216) SS BOND : bond 0.00023 / 0.01 ( 8) SS BOND : angle 0.44532 / 0.26 ( 16) hydrogen bonds : bond 0.05108 / 3.48 ( 1433) hydrogen bonds : angle 5.15410 / 3.76 ( 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 527 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 502 time to evaluate : 0.742 Fit side-chains REVERT: B 21 ARG cc_start: 0.8990 (ttt90) cc_final: 0.8662 (ttt-90) REVERT: B 49 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.6266 (mmt-90) REVERT: B 58 GLU cc_start: 0.9108 (pm20) cc_final: 0.8857 (pm20) REVERT: B 89 ASN cc_start: 0.8720 (t0) cc_final: 0.8502 (t0) REVERT: D 21 ARG cc_start: 0.8994 (ttt90) cc_final: 0.8673 (ttt-90) REVERT: D 49 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.6271 (mmt-90) REVERT: D 58 GLU cc_start: 0.9107 (pm20) cc_final: 0.8855 (pm20) REVERT: D 89 ASN cc_start: 0.8720 (t0) cc_final: 0.8503 (t0) REVERT: D 104 GLU cc_start: 0.9341 (tt0) cc_final: 0.9073 (tt0) REVERT: F 21 ARG cc_start: 0.8988 (ttt90) cc_final: 0.8660 (ttt-90) REVERT: F 58 GLU cc_start: 0.9108 (pm20) cc_final: 0.8860 (pm20) REVERT: F 89 ASN cc_start: 0.8718 (t0) cc_final: 0.8501 (t0) REVERT: F 104 GLU cc_start: 0.9341 (tt0) cc_final: 0.9072 (tt0) REVERT: H 21 ARG cc_start: 0.9003 (ttt90) cc_final: 0.8680 (ttt-90) REVERT: H 49 ARG cc_start: 0.7756 (mmt-90) cc_final: 0.6259 (mmt-90) REVERT: H 58 GLU cc_start: 0.9102 (pm20) cc_final: 0.8855 (pm20) REVERT: H 89 ASN cc_start: 0.8708 (t0) cc_final: 0.8486 (t0) REVERT: J 21 ARG cc_start: 0.8989 (ttt90) cc_final: 0.8660 (ttt-90) REVERT: J 58 GLU cc_start: 0.9106 (pm20) cc_final: 0.8858 (pm20) REVERT: J 89 ASN cc_start: 0.8716 (t0) cc_final: 0.8499 (t0) REVERT: J 104 GLU cc_start: 0.9347 (tt0) cc_final: 0.9077 (tt0) REVERT: L 21 ARG cc_start: 0.8985 (ttt90) cc_final: 0.8659 (ttt-90) REVERT: L 58 GLU cc_start: 0.9106 (pm20) cc_final: 0.8861 (pm20) REVERT: L 89 ASN cc_start: 0.8719 (t0) cc_final: 0.8501 (t0) REVERT: L 104 GLU cc_start: 0.9342 (tt0) cc_final: 0.9070 (tt0) REVERT: N 21 ARG cc_start: 0.8986 (ttt90) cc_final: 0.8659 (ttt-90) REVERT: N 58 GLU cc_start: 0.9101 (pm20) cc_final: 0.8849 (pm20) REVERT: N 89 ASN cc_start: 0.8709 (t0) cc_final: 0.8490 (t0) REVERT: P 21 ARG cc_start: 0.8988 (ttt90) cc_final: 0.8661 (ttt-90) REVERT: P 49 ARG cc_start: 0.7767 (mmt-90) cc_final: 0.6234 (mmt-90) REVERT: P 58 GLU cc_start: 0.9107 (pm20) cc_final: 0.8858 (pm20) REVERT: P 89 ASN cc_start: 0.8709 (t0) cc_final: 0.8492 (t0) outliers start: 25 outliers final: 9 residues processed: 511 average time/residue: 0.6959 time to fit residues: 395.8168 Evaluate side-chains 492 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 483 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 32 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 25 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 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: 5.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3224 r_free = 0.3224 target = 0.090757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.060449 restraints weight = 28953.176| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 1.87 r_work: 0.2501 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9323 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 23120 Z= 0.236 Angle : 0.595 6.672 31232 Z= 0.324 Chirality : 0.044 0.126 3448 Planarity : 0.004 0.026 3912 Dihedral : 12.360 61.753 4024 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.37 % Allowed : 14.51 % Favored : 84.12 % 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 are not related in a simple way. whole: 1.66 (0.16), residues: 2896 helix: 2.20 (0.13), residues: 1448 sheet: 0.98 (0.25), residues: 448 loop : -0.49 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 49 TYR 0.012 0.002 TYR B 42 PHE 0.013 0.002 PHE K 207 TRP 0.016 0.002 TRP O 14 HIS 0.003 0.001 HIS I 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (23112) covalent geometry : angle 0.59477 / 0.32 (31216) SS BOND : bond 0.00044 / 0.02 ( 8) SS BOND : angle 0.62925 / 0.38 ( 16) hydrogen bonds : bond 0.06964 / 4.76 ( 1433) hydrogen bonds : angle 5.41047 / 3.94 ( 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 528 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 498 time to evaluate : 0.858 Fit side-chains REVERT: B 49 ARG cc_start: 0.7962 (mmt-90) cc_final: 0.6430 (mmt-90) REVERT: B 58 GLU cc_start: 0.9112 (pm20) cc_final: 0.8792 (pm20) REVERT: B 77 ASP cc_start: 0.8418 (t0) cc_final: 0.8039 (t0) REVERT: B 80 ASN cc_start: 0.9115 (m-40) cc_final: 0.8867 (m110) REVERT: B 89 ASN cc_start: 0.8801 (t0) cc_final: 0.8530 (t0) REVERT: B 104 GLU cc_start: 0.9313 (tt0) cc_final: 0.9101 (tt0) REVERT: D 49 ARG cc_start: 0.7960 (mmt-90) cc_final: 0.6428 (mmt-90) REVERT: D 58 GLU cc_start: 0.9107 (pm20) cc_final: 0.8790 (pm20) REVERT: D 77 ASP cc_start: 0.8438 (t0) cc_final: 0.8063 (t0) REVERT: D 80 ASN cc_start: 0.9117 (m-40) cc_final: 0.8878 (m110) REVERT: D 89 ASN cc_start: 0.8808 (t0) cc_final: 0.8537 (t0) REVERT: D 104 GLU cc_start: 0.9321 (tt0) cc_final: 0.9093 (tt0) REVERT: F 49 ARG cc_start: 0.8044 (mmt-90) cc_final: 0.6517 (mmt-90) REVERT: F 58 GLU cc_start: 0.9107 (pm20) cc_final: 0.8789 (pm20) REVERT: F 77 ASP cc_start: 0.8440 (t0) cc_final: 0.8065 (t0) REVERT: F 80 ASN cc_start: 0.9119 (m-40) cc_final: 0.8878 (m110) REVERT: F 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8522 (t0) REVERT: F 104 GLU cc_start: 0.9320 (tt0) cc_final: 0.9090 (tt0) REVERT: H 49 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.6423 (mmt-90) REVERT: H 58 GLU cc_start: 0.9091 (pm20) cc_final: 0.8774 (pm20) REVERT: H 77 ASP cc_start: 0.8424 (t0) cc_final: 0.8050 (t0) REVERT: H 80 ASN cc_start: 0.9118 (m-40) cc_final: 0.8889 (m110) REVERT: H 89 ASN cc_start: 0.8795 (t0) cc_final: 0.8522 (t0) REVERT: H 104 GLU cc_start: 0.9318 (tt0) cc_final: 0.9115 (tt0) REVERT: J 58 GLU cc_start: 0.9108 (pm20) cc_final: 0.8790 (pm20) REVERT: J 77 ASP cc_start: 0.8427 (t0) cc_final: 0.8052 (t0) REVERT: J 80 ASN cc_start: 0.9116 (m-40) cc_final: 0.8878 (m110) REVERT: J 89 ASN cc_start: 0.8800 (t0) cc_final: 0.8527 (t0) REVERT: J 104 GLU cc_start: 0.9323 (tt0) cc_final: 0.9094 (tt0) REVERT: L 58 GLU cc_start: 0.9093 (pm20) cc_final: 0.8776 (pm20) REVERT: L 77 ASP cc_start: 0.8425 (t0) cc_final: 0.8050 (t0) REVERT: L 80 ASN cc_start: 0.9113 (m-40) cc_final: 0.8874 (m110) REVERT: L 89 ASN cc_start: 0.8799 (t0) cc_final: 0.8526 (t0) REVERT: L 104 GLU cc_start: 0.9320 (tt0) cc_final: 0.9090 (tt0) REVERT: N 58 GLU cc_start: 0.9104 (pm20) cc_final: 0.8785 (pm20) REVERT: N 77 ASP cc_start: 0.8418 (t0) cc_final: 0.8041 (t0) REVERT: N 80 ASN cc_start: 0.9110 (m-40) cc_final: 0.8865 (m110) REVERT: N 89 ASN cc_start: 0.8798 (t0) cc_final: 0.8525 (t0) REVERT: N 104 GLU cc_start: 0.9317 (tt0) cc_final: 0.9109 (tt0) REVERT: P 58 GLU cc_start: 0.9108 (pm20) cc_final: 0.8790 (pm20) REVERT: P 77 ASP cc_start: 0.8426 (t0) cc_final: 0.8049 (t0) REVERT: P 80 ASN cc_start: 0.9109 (m-40) cc_final: 0.8870 (m110) REVERT: P 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8522 (t0) REVERT: P 104 GLU cc_start: 0.9317 (tt0) cc_final: 0.9116 (tt0) outliers start: 30 outliers final: 18 residues processed: 508 average time/residue: 0.7023 time to fit residues: 399.8371 Evaluate side-chains 508 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 490 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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: 0.7980 chunk 213 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.063599 restraints weight = 28884.614| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 1.87 r_work: 0.2567 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9287 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23120 Z= 0.127 Angle : 0.523 5.527 31232 Z= 0.281 Chirality : 0.039 0.120 3448 Planarity : 0.004 0.032 3912 Dihedral : 12.005 61.176 4024 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.51 % Allowed : 14.28 % Favored : 84.22 % 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 are not related in a simple way. whole: 1.84 (0.16), residues: 2896 helix: 2.42 (0.14), residues: 1448 sheet: 0.91 (0.25), residues: 448 loop : -0.44 (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 C 223 PHE 0.011 0.001 PHE G 208 TRP 0.011 0.001 TRP I 14 HIS 0.002 0.000 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (23112) covalent geometry : angle 0.52285 / 0.28 (31216) SS BOND : bond 0.00026 / 0.01 ( 8) SS BOND : angle 0.37888 / 0.22 ( 16) hydrogen bonds : bond 0.05068 / 3.46 ( 1433) hydrogen bonds : angle 5.08957 / 3.71 ( 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 541 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 508 time to evaluate : 0.764 Fit side-chains REVERT: B 49 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.6455 (mmt-90) REVERT: B 58 GLU cc_start: 0.9149 (pm20) cc_final: 0.8830 (pm20) REVERT: B 77 ASP cc_start: 0.8421 (t0) cc_final: 0.8026 (t0) REVERT: B 80 ASN cc_start: 0.9098 (m-40) cc_final: 0.8863 (m110) REVERT: B 89 ASN cc_start: 0.8827 (t0) cc_final: 0.8517 (t0) REVERT: B 104 GLU cc_start: 0.9336 (tt0) cc_final: 0.9092 (tt0) REVERT: D 49 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.6464 (mmt-90) REVERT: D 58 GLU cc_start: 0.9143 (pm20) cc_final: 0.8821 (pm20) REVERT: D 77 ASP cc_start: 0.8434 (t0) cc_final: 0.8040 (t0) REVERT: D 80 ASN cc_start: 0.9103 (m-40) cc_final: 0.8853 (m110) REVERT: D 89 ASN cc_start: 0.8833 (t0) cc_final: 0.8525 (t0) REVERT: D 104 GLU cc_start: 0.9333 (tt0) cc_final: 0.9116 (tt0) REVERT: F 49 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.6494 (mmt-90) REVERT: F 58 GLU cc_start: 0.9146 (pm20) cc_final: 0.8825 (pm20) REVERT: F 77 ASP cc_start: 0.8422 (t0) cc_final: 0.8026 (t0) REVERT: F 80 ASN cc_start: 0.9099 (m-40) cc_final: 0.8846 (m110) REVERT: F 89 ASN cc_start: 0.8819 (t0) cc_final: 0.8509 (t0) REVERT: F 104 GLU cc_start: 0.9328 (tt0) cc_final: 0.9109 (tt0) REVERT: H 49 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.6451 (mmt-90) REVERT: H 58 GLU cc_start: 0.9140 (pm20) cc_final: 0.8819 (pm20) REVERT: H 77 ASP cc_start: 0.8416 (t0) cc_final: 0.8057 (t0) REVERT: H 89 ASN cc_start: 0.8820 (t0) cc_final: 0.8502 (t0) REVERT: H 104 GLU cc_start: 0.9343 (tt0) cc_final: 0.9101 (tt0) REVERT: J 58 GLU cc_start: 0.9152 (pm20) cc_final: 0.8833 (pm20) REVERT: J 77 ASP cc_start: 0.8414 (t0) cc_final: 0.8020 (t0) REVERT: J 80 ASN cc_start: 0.9094 (m-40) cc_final: 0.8848 (m110) REVERT: J 89 ASN cc_start: 0.8825 (t0) cc_final: 0.8514 (t0) REVERT: J 104 GLU cc_start: 0.9337 (tt0) cc_final: 0.9121 (tt0) REVERT: L 58 GLU cc_start: 0.9147 (pm20) cc_final: 0.8830 (pm20) REVERT: L 77 ASP cc_start: 0.8418 (t0) cc_final: 0.8025 (t0) REVERT: L 80 ASN cc_start: 0.9098 (m-40) cc_final: 0.8851 (m110) REVERT: L 89 ASN cc_start: 0.8825 (t0) cc_final: 0.8514 (t0) REVERT: L 104 GLU cc_start: 0.9331 (tt0) cc_final: 0.9112 (tt0) REVERT: N 58 GLU cc_start: 0.9141 (pm20) cc_final: 0.8818 (pm20) REVERT: N 77 ASP cc_start: 0.8406 (t0) cc_final: 0.8011 (t0) REVERT: N 80 ASN cc_start: 0.9090 (m-40) cc_final: 0.8857 (m110) REVERT: N 89 ASN cc_start: 0.8820 (t0) cc_final: 0.8508 (t0) REVERT: N 104 GLU cc_start: 0.9340 (tt0) cc_final: 0.9098 (tt0) REVERT: P 58 GLU cc_start: 0.9148 (pm20) cc_final: 0.8827 (pm20) REVERT: P 77 ASP cc_start: 0.8417 (t0) cc_final: 0.8030 (t0) REVERT: P 80 ASN cc_start: 0.9095 (m-40) cc_final: 0.8865 (m110) REVERT: P 89 ASN cc_start: 0.8823 (t0) cc_final: 0.8510 (t0) REVERT: P 104 GLU cc_start: 0.9337 (tt0) cc_final: 0.9096 (tt0) outliers start: 33 outliers final: 17 residues processed: 518 average time/residue: 0.6840 time to fit residues: 397.2641 Evaluate side-chains 507 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 490 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 283 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.090682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.061069 restraints weight = 28983.151| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 1.83 r_work: 0.2511 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9319 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 23120 Z= 0.212 Angle : 0.584 5.395 31232 Z= 0.316 Chirality : 0.043 0.123 3448 Planarity : 0.004 0.030 3912 Dihedral : 11.969 60.076 4024 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.80 % Favored : 97.93 % Rotamer: Outliers : 1.51 % Allowed : 14.14 % Favored : 84.35 % 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 are not related in a simple way. whole: 1.65 (0.16), residues: 2896 helix: 2.24 (0.14), residues: 1448 sheet: 0.89 (0.26), residues: 448 loop : -0.53 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 49 TYR 0.011 0.002 TYR N 42 PHE 0.013 0.002 PHE O 208 TRP 0.015 0.002 TRP I 14 HIS 0.003 0.001 HIS M 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (23112) covalent geometry : angle 0.58364 / 0.32 (31216) SS BOND : bond 0.00007 / 0.00 ( 8) SS BOND : angle 0.47147 / 0.28 ( 16) hydrogen bonds : bond 0.06580 / 4.50 ( 1433) hydrogen bonds : angle 5.34170 / 3.89 ( 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 537 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 504 time to evaluate : 0.759 Fit side-chains REVERT: B 49 ARG cc_start: 0.8009 (mmt-90) cc_final: 0.6546 (mmt-90) REVERT: B 58 GLU cc_start: 0.9128 (pm20) cc_final: 0.8841 (pm20) REVERT: B 77 ASP cc_start: 0.8461 (t0) cc_final: 0.8104 (t0) REVERT: B 80 ASN cc_start: 0.9103 (m-40) cc_final: 0.8896 (m110) REVERT: B 89 ASN cc_start: 0.8827 (t0) cc_final: 0.8523 (t0) REVERT: D 49 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.6546 (mmt-90) REVERT: D 58 GLU cc_start: 0.9122 (pm20) cc_final: 0.8832 (pm20) REVERT: D 77 ASP cc_start: 0.8484 (t0) cc_final: 0.8119 (t0) REVERT: D 80 ASN cc_start: 0.9105 (m-40) cc_final: 0.8880 (m110) REVERT: D 89 ASN cc_start: 0.8830 (t0) cc_final: 0.8518 (t0) REVERT: D 104 GLU cc_start: 0.9314 (tt0) cc_final: 0.9085 (tt0) REVERT: F 49 ARG cc_start: 0.8054 (mmt-90) cc_final: 0.6563 (mmt-90) REVERT: F 58 GLU cc_start: 0.9123 (pm20) cc_final: 0.8834 (pm20) REVERT: F 77 ASP cc_start: 0.8477 (t0) cc_final: 0.8112 (t0) REVERT: F 80 ASN cc_start: 0.9102 (m-40) cc_final: 0.8876 (m110) REVERT: F 89 ASN cc_start: 0.8825 (t0) cc_final: 0.8514 (t0) REVERT: F 104 GLU cc_start: 0.9314 (tt0) cc_final: 0.9085 (tt0) REVERT: H 49 ARG cc_start: 0.8011 (mmt-90) cc_final: 0.6543 (mmt-90) REVERT: H 58 GLU cc_start: 0.9120 (pm20) cc_final: 0.8752 (pm20) REVERT: H 77 ASP cc_start: 0.8457 (t0) cc_final: 0.8099 (t0) REVERT: H 80 ASN cc_start: 0.9104 (m-40) cc_final: 0.8896 (m110) REVERT: H 89 ASN cc_start: 0.8824 (t0) cc_final: 0.8507 (t0) REVERT: J 58 GLU cc_start: 0.9127 (pm20) cc_final: 0.8840 (pm20) REVERT: J 77 ASP cc_start: 0.8470 (t0) cc_final: 0.8104 (t0) REVERT: J 80 ASN cc_start: 0.9102 (m-40) cc_final: 0.8876 (m110) REVERT: J 89 ASN cc_start: 0.8830 (t0) cc_final: 0.8515 (t0) REVERT: J 104 GLU cc_start: 0.9320 (tt0) cc_final: 0.9092 (tt0) REVERT: L 58 GLU cc_start: 0.9128 (pm20) cc_final: 0.8760 (pm20) REVERT: L 77 ASP cc_start: 0.8476 (t0) cc_final: 0.8112 (t0) REVERT: L 80 ASN cc_start: 0.9101 (m-40) cc_final: 0.8877 (m110) REVERT: L 89 ASN cc_start: 0.8826 (t0) cc_final: 0.8511 (t0) REVERT: L 104 GLU cc_start: 0.9316 (tt0) cc_final: 0.9085 (tt0) REVERT: N 58 GLU cc_start: 0.9120 (pm20) cc_final: 0.8750 (pm20) REVERT: N 77 ASP cc_start: 0.8451 (t0) cc_final: 0.8094 (t0) REVERT: N 80 ASN cc_start: 0.9096 (m-40) cc_final: 0.8891 (m110) REVERT: N 89 ASN cc_start: 0.8826 (t0) cc_final: 0.8522 (t0) REVERT: P 58 GLU cc_start: 0.9127 (pm20) cc_final: 0.8841 (pm20) REVERT: P 77 ASP cc_start: 0.8466 (t0) cc_final: 0.8081 (t0) REVERT: P 80 ASN cc_start: 0.9097 (m-40) cc_final: 0.8874 (m110) REVERT: P 89 ASN cc_start: 0.8823 (t0) cc_final: 0.8510 (t0) outliers start: 33 outliers final: 18 residues processed: 521 average time/residue: 0.6553 time to fit residues: 383.4103 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 : 0.669 ------------------------------------------------------------------------------- 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: 3.9990 chunk 241 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 276 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.063547 restraints weight = 28706.459| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.86 r_work: 0.2566 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9288 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23120 Z= 0.124 Angle : 0.528 5.070 31232 Z= 0.283 Chirality : 0.039 0.118 3448 Planarity : 0.004 0.029 3912 Dihedral : 11.650 60.596 4024 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.04 % Favored : 97.69 % Rotamer: Outliers : 0.91 % Allowed : 15.10 % 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 are not related in a simple way. whole: 1.83 (0.16), residues: 2896 helix: 2.44 (0.14), residues: 1448 sheet: 0.84 (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 J 49 TYR 0.009 0.001 TYR K 223 PHE 0.011 0.001 PHE G 208 TRP 0.011 0.001 TRP I 14 HIS 0.002 0.001 HIS E 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (23112) covalent geometry : angle 0.52805 / 0.28 (31216) SS BOND : bond 0.00007 / 0.00 ( 8) SS BOND : angle 0.38103 / 0.22 ( 16) hydrogen bonds : bond 0.05044 / 3.44 ( 1433) hydrogen bonds : angle 5.08049 / 3.70 ( 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 521 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 501 time to evaluate : 0.730 Fit side-chains REVERT: B 49 ARG cc_start: 0.7977 (mmt-90) cc_final: 0.6403 (mmt-90) REVERT: B 58 GLU cc_start: 0.9185 (pm20) cc_final: 0.8834 (pm20) REVERT: B 77 ASP cc_start: 0.8431 (t0) cc_final: 0.8053 (t0) REVERT: B 80 ASN cc_start: 0.9074 (m-40) cc_final: 0.8823 (m110) REVERT: B 89 ASN cc_start: 0.8840 (t0) cc_final: 0.8502 (t0) REVERT: D 49 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.6404 (mmt-90) REVERT: D 58 GLU cc_start: 0.9183 (pm20) cc_final: 0.8833 (pm20) REVERT: D 77 ASP cc_start: 0.8441 (t0) cc_final: 0.8061 (t0) REVERT: D 80 ASN cc_start: 0.9074 (m-40) cc_final: 0.8802 (m110) REVERT: D 89 ASN cc_start: 0.8844 (t0) cc_final: 0.8512 (t0) REVERT: D 104 GLU cc_start: 0.9342 (tt0) cc_final: 0.9126 (tt0) REVERT: F 49 ARG cc_start: 0.8014 (mmt-90) cc_final: 0.6636 (mmt-90) REVERT: F 58 GLU cc_start: 0.9183 (pm20) cc_final: 0.8831 (pm20) REVERT: F 77 ASP cc_start: 0.8435 (t0) cc_final: 0.8053 (t0) REVERT: F 80 ASN cc_start: 0.9065 (m-40) cc_final: 0.8792 (m110) REVERT: F 89 ASN cc_start: 0.8834 (t0) cc_final: 0.8501 (t0) REVERT: F 104 GLU cc_start: 0.9339 (tt0) cc_final: 0.9121 (tt0) REVERT: H 49 ARG cc_start: 0.7977 (mmt-90) cc_final: 0.6406 (mmt-90) REVERT: H 58 GLU cc_start: 0.9175 (pm20) cc_final: 0.8824 (pm20) REVERT: H 77 ASP cc_start: 0.8424 (t0) cc_final: 0.8047 (t0) REVERT: H 80 ASN cc_start: 0.9066 (m-40) cc_final: 0.8820 (m110) REVERT: H 89 ASN cc_start: 0.8832 (t0) cc_final: 0.8492 (t0) REVERT: J 58 GLU cc_start: 0.9188 (pm20) cc_final: 0.8842 (pm20) REVERT: J 77 ASP cc_start: 0.8429 (t0) cc_final: 0.8048 (t0) REVERT: J 80 ASN cc_start: 0.9066 (m-40) cc_final: 0.8796 (m110) REVERT: J 89 ASN cc_start: 0.8842 (t0) cc_final: 0.8507 (t0) REVERT: J 104 GLU cc_start: 0.9344 (tt0) cc_final: 0.9126 (tt0) REVERT: L 58 GLU cc_start: 0.9184 (pm20) cc_final: 0.8838 (pm20) REVERT: L 77 ASP cc_start: 0.8429 (t0) cc_final: 0.8049 (t0) REVERT: L 80 ASN cc_start: 0.9075 (m-40) cc_final: 0.8806 (m110) REVERT: L 89 ASN cc_start: 0.8838 (t0) cc_final: 0.8502 (t0) REVERT: L 104 GLU cc_start: 0.9340 (tt0) cc_final: 0.9121 (tt0) REVERT: N 58 GLU cc_start: 0.9177 (pm20) cc_final: 0.8825 (pm20) REVERT: N 77 ASP cc_start: 0.8424 (t0) cc_final: 0.8043 (t0) REVERT: N 80 ASN cc_start: 0.9068 (m-40) cc_final: 0.8799 (m110) REVERT: N 89 ASN cc_start: 0.8839 (t0) cc_final: 0.8501 (t0) REVERT: P 58 GLU cc_start: 0.9185 (pm20) cc_final: 0.8835 (pm20) REVERT: P 77 ASP cc_start: 0.8432 (t0) cc_final: 0.8049 (t0) REVERT: P 80 ASN cc_start: 0.9065 (m-40) cc_final: 0.8793 (m110) REVERT: P 89 ASN cc_start: 0.8830 (t0) cc_final: 0.8495 (t0) outliers start: 20 outliers final: 20 residues processed: 511 average time/residue: 0.6684 time to fit residues: 381.0127 Evaluate side-chains 502 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 482 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain F residue 30 THR 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 K residue 50 MET Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain N residue 30 THR 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 48 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.091975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.061696 restraints weight = 28901.240| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 1.88 r_work: 0.2526 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9311 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23120 Z= 0.177 Angle : 0.572 5.813 31232 Z= 0.308 Chirality : 0.041 0.120 3448 Planarity : 0.004 0.028 3912 Dihedral : 11.546 60.264 4024 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.76 % Favored : 97.96 % Rotamer: Outliers : 1.28 % Allowed : 14.01 % Favored : 84.72 % 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 are not related in a simple way. whole: 1.71 (0.16), residues: 2896 helix: 2.32 (0.14), residues: 1448 sheet: 0.84 (0.26), residues: 448 loop : -0.51 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 49 TYR 0.011 0.001 TYR K 223 PHE 0.012 0.001 PHE A 208 TRP 0.013 0.001 TRP I 14 HIS 0.003 0.001 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (23112) covalent geometry : angle 0.57250 / 0.31 (31216) SS BOND : bond 0.00006 / 0.00 ( 8) SS BOND : angle 0.44467 / 0.26 ( 16) hydrogen bonds : bond 0.06005 / 4.10 ( 1433) hydrogen bonds : angle 5.24133 / 3.82 ( 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 523 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 495 time to evaluate : 0.758 Fit side-chains REVERT: B 49 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.6444 (mmt-90) REVERT: B 58 GLU cc_start: 0.9177 (pm20) cc_final: 0.8778 (pm20) REVERT: B 77 ASP cc_start: 0.8459 (t0) cc_final: 0.8109 (t0) REVERT: B 80 ASN cc_start: 0.9074 (m-40) cc_final: 0.8853 (m110) REVERT: B 89 ASN cc_start: 0.8821 (t0) cc_final: 0.8494 (t0) REVERT: D 49 ARG cc_start: 0.8007 (mmt-90) cc_final: 0.6453 (mmt-90) REVERT: D 58 GLU cc_start: 0.9176 (pm20) cc_final: 0.8776 (pm20) REVERT: D 77 ASP cc_start: 0.8480 (t0) cc_final: 0.8133 (t0) REVERT: D 80 ASN cc_start: 0.9073 (m-40) cc_final: 0.8852 (m110) REVERT: D 89 ASN cc_start: 0.8828 (t0) cc_final: 0.8492 (t0) REVERT: D 104 GLU cc_start: 0.9326 (tt0) cc_final: 0.9102 (tt0) REVERT: F 49 ARG cc_start: 0.8059 (mmt-90) cc_final: 0.6673 (mmt-90) REVERT: F 58 GLU cc_start: 0.9177 (pm20) cc_final: 0.8777 (pm20) REVERT: F 77 ASP cc_start: 0.8469 (t0) cc_final: 0.8120 (t0) REVERT: F 80 ASN cc_start: 0.9065 (m-40) cc_final: 0.8845 (m110) REVERT: F 89 ASN cc_start: 0.8818 (t0) cc_final: 0.8480 (t0) REVERT: F 104 GLU cc_start: 0.9326 (tt0) cc_final: 0.9102 (tt0) REVERT: H 49 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.6457 (mmt-90) REVERT: H 58 GLU cc_start: 0.9173 (pm20) cc_final: 0.8799 (pm20) REVERT: H 77 ASP cc_start: 0.8457 (t0) cc_final: 0.8104 (t0) REVERT: H 80 ASN cc_start: 0.9064 (m-40) cc_final: 0.8839 (m110) REVERT: H 89 ASN cc_start: 0.8797 (t0) cc_final: 0.8461 (t0) REVERT: J 58 GLU cc_start: 0.9178 (pm20) cc_final: 0.8779 (pm20) REVERT: J 77 ASP cc_start: 0.8461 (t0) cc_final: 0.8111 (t0) REVERT: J 80 ASN cc_start: 0.9069 (m-40) cc_final: 0.8846 (m110) REVERT: J 89 ASN cc_start: 0.8802 (t0) cc_final: 0.8469 (t0) REVERT: J 104 GLU cc_start: 0.9332 (tt0) cc_final: 0.9111 (tt0) REVERT: L 58 GLU cc_start: 0.9178 (pm20) cc_final: 0.8804 (pm20) REVERT: L 77 ASP cc_start: 0.8464 (t0) cc_final: 0.8086 (t0) REVERT: L 80 ASN cc_start: 0.9072 (m-40) cc_final: 0.8837 (m110) REVERT: L 89 ASN cc_start: 0.8800 (t0) cc_final: 0.8465 (t0) REVERT: L 104 GLU cc_start: 0.9323 (tt0) cc_final: 0.9096 (tt0) REVERT: N 58 GLU cc_start: 0.9169 (pm20) cc_final: 0.8767 (pm20) REVERT: N 77 ASP cc_start: 0.8448 (t0) cc_final: 0.8096 (t0) REVERT: N 80 ASN cc_start: 0.9066 (m-40) cc_final: 0.8847 (m110) REVERT: N 89 ASN cc_start: 0.8801 (t0) cc_final: 0.8468 (t0) REVERT: P 58 GLU cc_start: 0.9177 (pm20) cc_final: 0.8802 (pm20) REVERT: P 77 ASP cc_start: 0.8460 (t0) cc_final: 0.8107 (t0) REVERT: P 80 ASN cc_start: 0.9063 (m-40) cc_final: 0.8841 (m110) REVERT: P 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8461 (t0) outliers start: 28 outliers final: 27 residues processed: 506 average time/residue: 0.7039 time to fit residues: 397.6859 Evaluate side-chains 512 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 485 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 48 GLU 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: 2.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 280 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.062578 restraints weight = 28622.919| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 1.86 r_work: 0.2545 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23120 Z= 0.151 Angle : 0.556 6.020 31232 Z= 0.298 Chirality : 0.040 0.119 3448 Planarity : 0.004 0.028 3912 Dihedral : 11.422 60.608 4024 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.80 % Favored : 97.93 % Rotamer: Outliers : 1.23 % Allowed : 14.28 % Favored : 84.49 % 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 are not related in a simple way. whole: 1.76 (0.16), residues: 2896 helix: 2.38 (0.14), residues: 1448 sheet: 0.84 (0.26), residues: 448 loop : -0.50 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 49 TYR 0.010 0.001 TYR C 223 PHE 0.011 0.001 PHE A 208 TRP 0.012 0.001 TRP I 14 HIS 0.002 0.001 HIS K 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (23112) covalent geometry : angle 0.55645 / 0.30 (31216) SS BOND : bond 0.00005 / 0.00 ( 8) SS BOND : angle 0.41107 / 0.24 ( 16) hydrogen bonds : bond 0.05532 / 3.78 ( 1433) hydrogen bonds : angle 5.16965 / 3.76 ( 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 522 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 495 time to evaluate : 0.809 Fit side-chains REVERT: B 49 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.6526 (mmt-90) REVERT: B 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8761 (pm20) REVERT: B 77 ASP cc_start: 0.8456 (t0) cc_final: 0.8105 (t0) REVERT: B 80 ASN cc_start: 0.9056 (m-40) cc_final: 0.8821 (m110) REVERT: B 89 ASN cc_start: 0.8819 (t0) cc_final: 0.8479 (t0) REVERT: D 49 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.6539 (mmt-90) REVERT: D 58 GLU cc_start: 0.9158 (pm20) cc_final: 0.8757 (pm20) REVERT: D 77 ASP cc_start: 0.8462 (t0) cc_final: 0.8086 (t0) REVERT: D 80 ASN cc_start: 0.9046 (m-40) cc_final: 0.8797 (m110) REVERT: D 89 ASN cc_start: 0.8827 (t0) cc_final: 0.8493 (t0) REVERT: D 104 GLU cc_start: 0.9334 (tt0) cc_final: 0.9113 (tt0) REVERT: F 49 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.6676 (mmt-90) REVERT: F 58 GLU cc_start: 0.9160 (pm20) cc_final: 0.8760 (pm20) REVERT: F 77 ASP cc_start: 0.8459 (t0) cc_final: 0.8081 (t0) REVERT: F 80 ASN cc_start: 0.9045 (m-40) cc_final: 0.8794 (m110) REVERT: F 89 ASN cc_start: 0.8818 (t0) cc_final: 0.8482 (t0) REVERT: F 104 GLU cc_start: 0.9335 (tt0) cc_final: 0.9114 (tt0) REVERT: H 49 ARG cc_start: 0.8007 (mmt-90) cc_final: 0.6538 (mmt-90) REVERT: H 58 GLU cc_start: 0.9171 (pm20) cc_final: 0.8805 (pm20) REVERT: H 77 ASP cc_start: 0.8451 (t0) cc_final: 0.8103 (t0) REVERT: H 80 ASN cc_start: 0.9044 (m-40) cc_final: 0.8818 (m110) REVERT: H 89 ASN cc_start: 0.8800 (t0) cc_final: 0.8461 (t0) REVERT: J 58 GLU cc_start: 0.9164 (pm20) cc_final: 0.8764 (pm20) REVERT: J 77 ASP cc_start: 0.8450 (t0) cc_final: 0.8072 (t0) REVERT: J 80 ASN cc_start: 0.9045 (m-40) cc_final: 0.8793 (m110) REVERT: J 89 ASN cc_start: 0.8807 (t0) cc_final: 0.8468 (t0) REVERT: J 104 GLU cc_start: 0.9331 (tt0) cc_final: 0.9108 (tt0) REVERT: L 58 GLU cc_start: 0.9159 (pm20) cc_final: 0.8788 (pm20) REVERT: L 77 ASP cc_start: 0.8450 (t0) cc_final: 0.8071 (t0) REVERT: L 80 ASN cc_start: 0.9046 (m-40) cc_final: 0.8799 (m110) REVERT: L 89 ASN cc_start: 0.8808 (t0) cc_final: 0.8467 (t0) REVERT: L 104 GLU cc_start: 0.9330 (tt0) cc_final: 0.9106 (tt0) REVERT: N 58 GLU cc_start: 0.9153 (pm20) cc_final: 0.8749 (pm20) REVERT: N 77 ASP cc_start: 0.8443 (t0) cc_final: 0.8062 (t0) REVERT: N 80 ASN cc_start: 0.9047 (m-40) cc_final: 0.8800 (m110) REVERT: N 89 ASN cc_start: 0.8806 (t0) cc_final: 0.8468 (t0) REVERT: P 58 GLU cc_start: 0.9164 (pm20) cc_final: 0.8763 (pm20) REVERT: P 77 ASP cc_start: 0.8448 (t0) cc_final: 0.8067 (t0) REVERT: P 80 ASN cc_start: 0.9042 (m-40) cc_final: 0.8791 (m110) REVERT: P 89 ASN cc_start: 0.8804 (t0) cc_final: 0.8466 (t0) outliers start: 27 outliers final: 19 residues processed: 505 average time/residue: 0.6918 time to fit residues: 389.8410 Evaluate side-chains 503 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 484 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 48 GLU 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: 1.9990 chunk 279 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.061127 restraints weight = 28955.275| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 1.87 r_work: 0.2515 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9316 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 23120 Z= 0.201 Angle : 0.596 6.412 31232 Z= 0.321 Chirality : 0.042 0.122 3448 Planarity : 0.004 0.027 3912 Dihedral : 11.461 60.299 4024 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.28 % Allowed : 14.51 % Favored : 84.22 % 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 are not related in a simple way. whole: 1.64 (0.16), residues: 2896 helix: 2.26 (0.14), residues: 1448 sheet: 0.85 (0.26), residues: 448 loop : -0.55 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 49 TYR 0.011 0.001 TYR P 42 PHE 0.013 0.001 PHE O 208 TRP 0.014 0.002 TRP I 14 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (23112) covalent geometry : angle 0.59615 / 0.32 (31216) SS BOND : bond 0.00009 / 0.00 ( 8) SS BOND : angle 0.45262 / 0.27 ( 16) hydrogen bonds : bond 0.06347 / 4.34 ( 1433) hydrogen bonds : angle 5.31678 / 3.87 ( 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 528 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 500 time to evaluate : 0.845 Fit side-chains REVERT: B 49 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.6559 (mmt-90) REVERT: B 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8849 (pm20) REVERT: B 77 ASP cc_start: 0.8459 (t0) cc_final: 0.8101 (t0) REVERT: B 80 ASN cc_start: 0.9034 (m-40) cc_final: 0.8782 (m110) REVERT: B 89 ASN cc_start: 0.8832 (t0) cc_final: 0.8508 (t0) REVERT: D 49 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.6565 (mmt-90) REVERT: D 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8851 (pm20) REVERT: D 77 ASP cc_start: 0.8481 (t0) cc_final: 0.8129 (t0) REVERT: D 80 ASN cc_start: 0.9036 (m-40) cc_final: 0.8788 (m110) REVERT: D 89 ASN cc_start: 0.8824 (t0) cc_final: 0.8499 (t0) REVERT: F 49 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.6690 (mmt-90) REVERT: F 58 GLU cc_start: 0.9163 (pm20) cc_final: 0.8854 (pm20) REVERT: F 77 ASP cc_start: 0.8465 (t0) cc_final: 0.8109 (t0) REVERT: F 80 ASN cc_start: 0.9032 (m-40) cc_final: 0.8781 (m110) REVERT: F 89 ASN cc_start: 0.8824 (t0) cc_final: 0.8506 (t0) REVERT: H 49 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.6562 (mmt-90) REVERT: H 58 GLU cc_start: 0.9163 (pm20) cc_final: 0.8854 (pm20) REVERT: H 77 ASP cc_start: 0.8461 (t0) cc_final: 0.8107 (t0) REVERT: H 80 ASN cc_start: 0.9035 (m-40) cc_final: 0.8798 (m110) REVERT: H 89 ASN cc_start: 0.8804 (t0) cc_final: 0.8472 (t0) REVERT: J 58 GLU cc_start: 0.9163 (pm20) cc_final: 0.8854 (pm20) REVERT: J 77 ASP cc_start: 0.8463 (t0) cc_final: 0.8108 (t0) REVERT: J 80 ASN cc_start: 0.9028 (m-40) cc_final: 0.8778 (m110) REVERT: J 89 ASN cc_start: 0.8811 (t0) cc_final: 0.8481 (t0) REVERT: L 58 GLU cc_start: 0.9170 (pm20) cc_final: 0.8862 (pm20) REVERT: L 77 ASP cc_start: 0.8462 (t0) cc_final: 0.8106 (t0) REVERT: L 80 ASN cc_start: 0.9031 (m-40) cc_final: 0.8784 (m110) REVERT: L 89 ASN cc_start: 0.8808 (t0) cc_final: 0.8475 (t0) REVERT: N 58 GLU cc_start: 0.9155 (pm20) cc_final: 0.8844 (pm20) REVERT: N 77 ASP cc_start: 0.8458 (t0) cc_final: 0.8105 (t0) REVERT: N 80 ASN cc_start: 0.9033 (m-40) cc_final: 0.8789 (m110) REVERT: N 89 ASN cc_start: 0.8810 (t0) cc_final: 0.8479 (t0) REVERT: P 58 GLU cc_start: 0.9161 (pm20) cc_final: 0.8849 (pm20) REVERT: P 77 ASP cc_start: 0.8459 (t0) cc_final: 0.8101 (t0) REVERT: P 80 ASN cc_start: 0.9023 (m-40) cc_final: 0.8775 (m110) REVERT: P 89 ASN cc_start: 0.8807 (t0) cc_final: 0.8476 (t0) outliers start: 28 outliers final: 20 residues processed: 510 average time/residue: 0.6776 time to fit residues: 386.9856 Evaluate side-chains 509 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 489 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 48 GLU 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 48 GLU 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: 0.9980 chunk 146 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 57 optimal weight: 0.4980 chunk 218 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.064419 restraints weight = 28713.559| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 1.86 r_work: 0.2583 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23120 Z= 0.119 Angle : 0.538 6.820 31232 Z= 0.287 Chirality : 0.039 0.117 3448 Planarity : 0.004 0.027 3912 Dihedral : 11.199 61.471 4024 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.07 % Favored : 97.65 % Rotamer: Outliers : 1.23 % Allowed : 14.42 % Favored : 84.35 % 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 are not related in a simple way. whole: 1.84 (0.16), residues: 2896 helix: 2.49 (0.14), residues: 1448 sheet: 0.79 (0.25), residues: 448 loop : -0.49 (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 C 223 PHE 0.011 0.001 PHE I 208 TRP 0.010 0.001 TRP A 14 HIS 0.002 0.001 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (23112) covalent geometry : angle 0.53800 / 0.29 (31216) SS BOND : bond 0.00029 / 0.01 ( 8) SS BOND : angle 0.36584 / 0.21 ( 16) hydrogen bonds : bond 0.04721 / 3.22 ( 1433) hydrogen bonds : angle 5.02449 / 3.66 ( 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 535 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 508 time to evaluate : 0.515 Fit side-chains REVERT: B 49 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.6523 (mmt-90) REVERT: B 58 GLU cc_start: 0.9169 (pm20) cc_final: 0.8814 (pm20) REVERT: B 77 ASP cc_start: 0.8416 (t0) cc_final: 0.8037 (t0) REVERT: B 80 ASN cc_start: 0.8966 (m-40) cc_final: 0.8736 (m110) REVERT: B 89 ASN cc_start: 0.8839 (t0) cc_final: 0.8520 (t0) REVERT: D 49 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.6537 (mmt-90) REVERT: D 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8815 (pm20) REVERT: D 77 ASP cc_start: 0.8423 (t0) cc_final: 0.8040 (t0) REVERT: D 80 ASN cc_start: 0.8964 (m-40) cc_final: 0.8714 (m110) REVERT: D 89 ASN cc_start: 0.8824 (t0) cc_final: 0.8505 (t0) REVERT: F 49 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.6565 (mmt-90) REVERT: F 58 GLU cc_start: 0.9169 (pm20) cc_final: 0.8814 (pm20) REVERT: F 77 ASP cc_start: 0.8425 (t0) cc_final: 0.8049 (t0) REVERT: F 80 ASN cc_start: 0.8970 (m-40) cc_final: 0.8740 (m110) REVERT: F 89 ASN cc_start: 0.8843 (t0) cc_final: 0.8508 (t0) REVERT: H 49 ARG cc_start: 0.8025 (mmt-90) cc_final: 0.6532 (mmt-90) REVERT: H 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8808 (pm20) REVERT: H 77 ASP cc_start: 0.8410 (t0) cc_final: 0.8026 (t0) REVERT: H 80 ASN cc_start: 0.8963 (m-40) cc_final: 0.8718 (m110) REVERT: H 89 ASN cc_start: 0.8821 (t0) cc_final: 0.8471 (t0) REVERT: J 58 GLU cc_start: 0.9172 (pm20) cc_final: 0.8822 (pm20) REVERT: J 77 ASP cc_start: 0.8417 (t0) cc_final: 0.8034 (t0) REVERT: J 80 ASN cc_start: 0.8968 (m-40) cc_final: 0.8719 (m110) REVERT: J 89 ASN cc_start: 0.8827 (t0) cc_final: 0.8479 (t0) REVERT: L 58 GLU cc_start: 0.9172 (pm20) cc_final: 0.8823 (pm20) REVERT: L 77 ASP cc_start: 0.8411 (t0) cc_final: 0.8027 (t0) REVERT: L 80 ASN cc_start: 0.8968 (m-40) cc_final: 0.8719 (m110) REVERT: L 89 ASN cc_start: 0.8827 (t0) cc_final: 0.8477 (t0) REVERT: N 58 GLU cc_start: 0.9164 (pm20) cc_final: 0.8810 (pm20) REVERT: N 77 ASP cc_start: 0.8408 (t0) cc_final: 0.8032 (t0) REVERT: N 80 ASN cc_start: 0.8965 (m-40) cc_final: 0.8733 (m110) REVERT: N 89 ASN cc_start: 0.8824 (t0) cc_final: 0.8476 (t0) REVERT: P 58 GLU cc_start: 0.9170 (pm20) cc_final: 0.8816 (pm20) REVERT: P 77 ASP cc_start: 0.8414 (t0) cc_final: 0.8035 (t0) REVERT: P 80 ASN cc_start: 0.8962 (m-40) cc_final: 0.8732 (m110) REVERT: P 89 ASN cc_start: 0.8818 (t0) cc_final: 0.8470 (t0) outliers start: 27 outliers final: 19 residues processed: 518 average time/residue: 0.6566 time to fit residues: 379.8652 Evaluate side-chains 513 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 494 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 48 GLU 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: 9.9990 chunk 72 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 228 optimal weight: 0.0980 chunk 256 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.092016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.061726 restraints weight = 28922.256| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 1.87 r_work: 0.2526 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9310 moved from start: 0.1240 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= 0.181 Angle : 0.588 6.787 31232 Z= 0.316 Chirality : 0.041 0.121 3448 Planarity : 0.004 0.027 3912 Dihedral : 11.248 61.044 4024 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 0.82 % Allowed : 15.28 % Favored : 83.90 % 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 are not related in a simple way. whole: 1.67 (0.16), residues: 2896 helix: 2.31 (0.14), residues: 1448 sheet: 0.78 (0.26), residues: 448 loop : -0.53 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 49 TYR 0.011 0.001 TYR C 223 PHE 0.012 0.001 PHE E 208 TRP 0.014 0.002 TRP O 14 HIS 0.003 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (23112) covalent geometry : angle 0.58768 / 0.32 (31216) SS BOND : bond 0.00009 / 0.01 ( 8) SS BOND : angle 0.46018 / 0.27 ( 16) hydrogen bonds : bond 0.06042 / 4.13 ( 1433) hydrogen bonds : angle 5.25492 / 3.83 ( 4107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11225.89 seconds wall clock time: 190 minutes 34.29 seconds (11434.29 seconds total)