Starting phenix.real_space_refine on Fri May 23 01:31:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy6_42793/05_2025/8uy6_42793_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy6_42793/05_2025/8uy6_42793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uy6_42793/05_2025/8uy6_42793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy6_42793/05_2025/8uy6_42793.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy6_42793/05_2025/8uy6_42793_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy6_42793/05_2025/8uy6_42793_trim.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.36, per 1000 atoms: 0.55 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: 5.95 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.62 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: 7.39 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3673 1.32 - 1.44: 6179 1.44 - 1.56: 13052 1.56 - 1.69: 32 1.69 - 1.81: 176 Bond restraints: 23112 Sorted by residual: bond pdb=" CB ASN P 89 " pdb=" CG ASN P 89 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.41e-01 bond pdb=" CB ASN N 89 " pdb=" CG ASN N 89 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.29e-01 bond pdb=" CB ASN B 89 " pdb=" CG ASN B 89 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.27e-01 bond pdb=" CB ASN D 89 " pdb=" CG ASN D 89 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.70e-01 bond pdb=" CB ASN J 89 " pdb=" CG ASN J 89 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.70e-01 ... (remaining 23107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 30727 1.70 - 3.39: 385 3.39 - 5.09: 64 5.09 - 6.78: 32 6.78 - 8.48: 8 Bond angle restraints: 31216 Sorted by residual: angle pdb=" CB2 CDL O 301 " pdb=" C1 CDL O 301 " pdb=" CA2 CDL O 301 " ideal model delta sigma weight residual 113.28 104.80 8.48 3.06e+00 1.07e-01 7.66e+00 angle pdb=" CB2 CDL G 301 " pdb=" C1 CDL G 301 " pdb=" CA2 CDL G 301 " ideal model delta sigma weight residual 113.28 104.83 8.45 3.06e+00 1.07e-01 7.60e+00 angle pdb=" CB2 CDL E 301 " pdb=" C1 CDL E 301 " pdb=" CA2 CDL E 301 " ideal model delta sigma weight residual 113.28 104.84 8.44 3.06e+00 1.07e-01 7.60e+00 angle pdb=" CB2 CDL A 301 " pdb=" C1 CDL A 301 " pdb=" CA2 CDL A 301 " ideal model delta sigma weight residual 113.28 104.84 8.44 3.06e+00 1.07e-01 7.60e+00 angle pdb=" CB2 CDL M 301 " pdb=" C1 CDL M 301 " pdb=" CA2 CDL M 301 " ideal model delta sigma weight residual 113.28 104.84 8.44 3.06e+00 1.07e-01 7.60e+00 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.13: 12706 29.13 - 58.27: 759 58.27 - 87.40: 31 87.40 - 116.54: 0 116.54 - 145.67: 8 Dihedral angle restraints: 13504 sinusoidal: 5424 harmonic: 8080 Sorted by residual: dihedral pdb=" CA5 CDL C 301 " pdb=" CA4 CDL C 301 " pdb=" OA6 CDL C 301 " pdb=" CA6 CDL C 301 " ideal model delta sinusoidal sigma weight residual 168.24 -46.09 -145.67 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA5 CDL G 301 " pdb=" CA4 CDL G 301 " pdb=" OA6 CDL G 301 " pdb=" CA6 CDL G 301 " ideal model delta sinusoidal sigma weight residual 168.24 -46.09 -145.67 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA5 CDL E 301 " pdb=" CA4 CDL E 301 " pdb=" OA6 CDL E 301 " pdb=" CA6 CDL E 301 " ideal model delta sinusoidal sigma weight residual 168.24 -46.10 -145.66 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 13501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3169 0.067 - 0.135: 263 0.135 - 0.202: 0 0.202 - 0.269: 0 0.269 - 0.336: 16 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CB4 CDL G 301 " pdb=" CB3 CDL G 301 " pdb=" CB6 CDL G 301 " pdb=" OB6 CDL G 301 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB4 CDL O 301 " pdb=" CB3 CDL O 301 " pdb=" CB6 CDL O 301 " pdb=" OB6 CDL O 301 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB4 CDL E 301 " pdb=" CB3 CDL E 301 " pdb=" CB6 CDL E 301 " pdb=" OB6 CDL E 301 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 3445 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 88 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C GLN C 88 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN C 88 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 89 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN O 88 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLN O 88 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN O 88 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL O 89 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN M 88 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C GLN M 88 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN M 88 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL M 89 " 0.010 2.00e-02 2.50e+03 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 148 2.60 - 3.18: 19521 3.18 - 3.75: 34940 3.75 - 4.33: 52004 4.33 - 4.90: 84810 Nonbonded interactions: 191423 Sorted by model distance: nonbonded pdb=" N GLN P 15 " pdb=" OE1 GLN P 15 " model vdw 2.025 3.120 nonbonded pdb=" N GLN F 15 " pdb=" OE1 GLN F 15 " model vdw 2.026 3.120 nonbonded pdb=" N GLN D 15 " pdb=" OE1 GLN D 15 " model vdw 2.026 3.120 nonbonded pdb=" N GLN L 15 " pdb=" OE1 GLN L 15 " model vdw 2.026 3.120 nonbonded pdb=" N GLN B 15 " pdb=" OE1 GLN B 15 " model vdw 2.026 3.120 ... (remaining 191418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.19 Found NCS groups: 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' } 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' } 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: 3.570 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 47.910 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 23120 Z= 0.133 Angle : 0.533 8.477 31232 Z= 0.284 Chirality : 0.042 0.336 3448 Planarity : 0.004 0.019 3912 Dihedral : 17.149 145.669 8392 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.59 % Favored : 96.13 % Rotamer: Outliers : 1.00 % Allowed : 15.78 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (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 TRP 0.010 0.001 TRP I 14 HIS 0.002 0.001 HIS P 101 PHE 0.010 0.001 PHE A 208 TYR 0.009 0.001 TYR G 223 ARG 0.002 0.000 ARG J 49 Details of bonding type rmsd hydrogen bonds : bond 0.10979 ( 1433) hydrogen bonds : angle 7.08282 ( 4107) SS BOND : bond 0.00020 ( 8) SS BOND : angle 0.44003 ( 16) covalent geometry : bond 0.00265 (23112) covalent geometry : angle 0.53257 (31216) *********************** 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 : 2.431 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 534 average time/residue: 1.6340 time to fit residues: 971.6793 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 : 2.560 ------------------------------------------------------------------------------- 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 243 optimal weight: 0.6980 chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN B 80 ASN D 69 GLN D 80 ASN F 69 GLN F 80 ASN H 69 GLN H 80 ASN J 69 GLN J 80 ASN L 69 GLN L 80 ASN N 69 GLN N 80 ASN P 69 GLN P 80 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.065437 restraints weight = 28800.154| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 1.85 r_work: 0.2606 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 23120 Z= 0.118 Angle : 0.515 4.691 31232 Z= 0.277 Chirality : 0.039 0.116 3448 Planarity : 0.004 0.038 3912 Dihedral : 14.011 150.059 3918 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.93 % Favored : 97.79 % Rotamer: Outliers : 1.46 % Allowed : 15.37 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 2896 helix: 2.36 (0.14), residues: 1448 sheet: 0.98 (0.24), residues: 448 loop : -0.25 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 14 HIS 0.002 0.001 HIS M 124 PHE 0.009 0.001 PHE K 207 TYR 0.009 0.001 TYR O 223 ARG 0.007 0.001 ARG J 49 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 1433) hydrogen bonds : angle 5.08195 ( 4107) SS BOND : bond 0.00025 ( 8) SS BOND : angle 0.39558 ( 16) covalent geometry : bond 0.00224 (23112) covalent geometry : angle 0.51477 (31216) *********************** 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 541 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 509 time to evaluate : 2.355 Fit side-chains REVERT: B 21 ARG cc_start: 0.8989 (ttt90) cc_final: 0.8640 (ttt-90) REVERT: B 49 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.6214 (mmt-90) REVERT: B 58 GLU cc_start: 0.9093 (pm20) cc_final: 0.8844 (pm20) REVERT: B 89 ASN cc_start: 0.8695 (t0) cc_final: 0.8486 (t0) REVERT: D 21 ARG cc_start: 0.8990 (ttt90) cc_final: 0.8646 (ttt-90) REVERT: D 49 ARG cc_start: 0.7702 (mmt-90) cc_final: 0.6218 (mmt-90) REVERT: D 58 GLU cc_start: 0.9093 (pm20) cc_final: 0.8844 (pm20) REVERT: D 89 ASN cc_start: 0.8696 (t0) cc_final: 0.8472 (t0) REVERT: D 104 GLU cc_start: 0.9344 (tt0) cc_final: 0.9089 (tt0) REVERT: F 21 ARG cc_start: 0.8986 (ttt90) cc_final: 0.8642 (ttt-90) REVERT: F 49 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.6211 (mmt-90) REVERT: F 58 GLU cc_start: 0.9098 (pm20) cc_final: 0.8853 (pm20) REVERT: F 89 ASN cc_start: 0.8699 (t0) cc_final: 0.8475 (t0) REVERT: F 104 GLU cc_start: 0.9345 (tt0) cc_final: 0.9090 (tt0) REVERT: H 21 ARG cc_start: 0.8999 (ttt90) cc_final: 0.8649 (ttt-90) REVERT: H 49 ARG cc_start: 0.7696 (mmt-90) cc_final: 0.6208 (mmt-90) REVERT: H 58 GLU cc_start: 0.9086 (pm20) cc_final: 0.8840 (pm20) REVERT: H 89 ASN cc_start: 0.8691 (t0) cc_final: 0.8479 (t0) REVERT: J 21 ARG cc_start: 0.8986 (ttt90) cc_final: 0.8643 (ttt-90) REVERT: J 58 GLU cc_start: 0.9094 (pm20) cc_final: 0.8848 (pm20) REVERT: J 89 ASN cc_start: 0.8693 (t0) cc_final: 0.8469 (t0) REVERT: J 104 GLU cc_start: 0.9346 (tt0) cc_final: 0.9090 (tt0) REVERT: L 21 ARG cc_start: 0.8981 (ttt90) cc_final: 0.8634 (ttt-90) REVERT: L 58 GLU cc_start: 0.9091 (pm20) cc_final: 0.8849 (pm20) REVERT: L 89 ASN cc_start: 0.8695 (t0) cc_final: 0.8470 (t0) REVERT: L 104 GLU cc_start: 0.9339 (tt0) cc_final: 0.9083 (tt0) REVERT: N 21 ARG cc_start: 0.8983 (ttt90) cc_final: 0.8637 (ttt-90) REVERT: N 58 GLU cc_start: 0.9091 (pm20) cc_final: 0.8843 (pm20) REVERT: N 89 ASN cc_start: 0.8684 (t0) cc_final: 0.8472 (t0) REVERT: P 21 ARG cc_start: 0.8982 (ttt90) cc_final: 0.8638 (ttt-90) REVERT: P 58 GLU cc_start: 0.9097 (pm20) cc_final: 0.8851 (pm20) REVERT: P 89 ASN cc_start: 0.8683 (t0) cc_final: 0.8459 (t0) outliers start: 32 outliers final: 8 residues processed: 517 average time/residue: 1.6543 time to fit residues: 949.8170 Evaluate side-chains 501 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 493 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain P residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 63 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 28 optimal weight: 0.0030 chunk 265 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN D 80 ASN F 80 ASN H 80 ASN J 80 ASN L 80 ASN N 80 ASN P 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.062640 restraints weight = 28831.384| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 1.83 r_work: 0.2545 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.0901 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= 0.169 Angle : 0.550 6.690 31232 Z= 0.296 Chirality : 0.041 0.118 3448 Planarity : 0.004 0.026 3912 Dihedral : 13.918 150.889 3896 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.93 % Favored : 97.79 % Rotamer: Outliers : 1.55 % Allowed : 15.42 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 2896 helix: 2.37 (0.13), residues: 1448 sheet: 0.94 (0.25), residues: 448 loop : -0.36 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 14 HIS 0.003 0.001 HIS I 124 PHE 0.011 0.001 PHE G 208 TYR 0.010 0.001 TYR G 223 ARG 0.007 0.001 ARG N 49 Details of bonding type rmsd hydrogen bonds : bond 0.05910 ( 1433) hydrogen bonds : angle 5.20184 ( 4107) SS BOND : bond 0.00044 ( 8) SS BOND : angle 0.53256 ( 16) covalent geometry : bond 0.00390 (23112) covalent geometry : angle 0.54987 (31216) *********************** 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 533 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 499 time to evaluate : 2.222 Fit side-chains REVERT: B 21 ARG cc_start: 0.8971 (ttt90) cc_final: 0.8633 (ttt-90) REVERT: B 49 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.6332 (mmt-90) REVERT: B 58 GLU cc_start: 0.9116 (pm20) cc_final: 0.8748 (pm20) REVERT: B 89 ASN cc_start: 0.8766 (t0) cc_final: 0.8490 (t0) REVERT: B 104 GLU cc_start: 0.9333 (tt0) cc_final: 0.9072 (tt0) REVERT: D 21 ARG cc_start: 0.8975 (ttt90) cc_final: 0.8642 (ttt-90) REVERT: D 49 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.6321 (mmt-90) REVERT: D 58 GLU cc_start: 0.9102 (pm20) cc_final: 0.8731 (pm20) REVERT: D 89 ASN cc_start: 0.8765 (t0) cc_final: 0.8499 (t0) REVERT: F 21 ARG cc_start: 0.8974 (ttt90) cc_final: 0.8645 (ttt-90) REVERT: F 49 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.6323 (mmt-90) REVERT: F 58 GLU cc_start: 0.9104 (pm20) cc_final: 0.8735 (pm20) REVERT: F 89 ASN cc_start: 0.8755 (t0) cc_final: 0.8489 (t0) REVERT: H 21 ARG cc_start: 0.8988 (ttt90) cc_final: 0.8648 (ttt-90) REVERT: H 49 ARG cc_start: 0.7903 (mmt-90) cc_final: 0.6320 (mmt-90) REVERT: H 89 ASN cc_start: 0.8760 (t0) cc_final: 0.8481 (t0) REVERT: H 104 GLU cc_start: 0.9344 (tt0) cc_final: 0.9117 (tt0) REVERT: J 21 ARG cc_start: 0.8978 (ttt90) cc_final: 0.8645 (ttt-90) REVERT: J 58 GLU cc_start: 0.9103 (pm20) cc_final: 0.8735 (pm20) REVERT: J 89 ASN cc_start: 0.8760 (t0) cc_final: 0.8493 (t0) REVERT: L 21 ARG cc_start: 0.8973 (ttt90) cc_final: 0.8637 (ttt-90) REVERT: L 89 ASN cc_start: 0.8760 (t0) cc_final: 0.8493 (t0) REVERT: N 21 ARG cc_start: 0.8980 (ttt90) cc_final: 0.8641 (ttt-90) REVERT: N 58 GLU cc_start: 0.9108 (pm20) cc_final: 0.8736 (pm20) REVERT: N 89 ASN cc_start: 0.8758 (t0) cc_final: 0.8478 (t0) REVERT: N 104 GLU cc_start: 0.9343 (tt0) cc_final: 0.9086 (tt0) REVERT: P 21 ARG cc_start: 0.8971 (ttt90) cc_final: 0.8635 (ttt-90) REVERT: P 58 GLU cc_start: 0.9104 (pm20) cc_final: 0.8734 (pm20) REVERT: P 89 ASN cc_start: 0.8753 (t0) cc_final: 0.8478 (t0) REVERT: P 104 GLU cc_start: 0.9333 (tt0) cc_final: 0.9103 (tt0) outliers start: 34 outliers final: 18 residues processed: 509 average time/residue: 1.5308 time to fit residues: 871.4514 Evaluate side-chains 499 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 481 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 242 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 232 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN D 80 ASN F 80 ASN H 80 ASN J 80 ASN L 80 ASN N 80 ASN P 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.062981 restraints weight = 28972.498| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 1.83 r_work: 0.2553 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.0996 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= 0.150 Angle : 0.538 6.800 31232 Z= 0.288 Chirality : 0.040 0.119 3448 Planarity : 0.004 0.029 3912 Dihedral : 13.707 151.393 3896 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.55 % Allowed : 13.91 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 2896 helix: 2.39 (0.14), residues: 1448 sheet: 0.91 (0.25), residues: 448 loop : -0.40 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 14 HIS 0.002 0.001 HIS H 101 PHE 0.011 0.001 PHE E 196 TYR 0.010 0.001 TYR G 223 ARG 0.005 0.001 ARG P 49 Details of bonding type rmsd hydrogen bonds : bond 0.05533 ( 1433) hydrogen bonds : angle 5.14340 ( 4107) SS BOND : bond 0.00027 ( 8) SS BOND : angle 0.46924 ( 16) covalent geometry : bond 0.00338 (23112) covalent geometry : angle 0.53769 (31216) *********************** 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 528 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 494 time to evaluate : 2.390 Fit side-chains REVERT: B 49 ARG cc_start: 0.7931 (mmt-90) cc_final: 0.6478 (mmt-90) REVERT: B 58 GLU cc_start: 0.9153 (pm20) cc_final: 0.8832 (pm20) REVERT: B 77 ASP cc_start: 0.8431 (t0) cc_final: 0.8062 (t0) REVERT: B 80 ASN cc_start: 0.9112 (m-40) cc_final: 0.8882 (m110) REVERT: B 89 ASN cc_start: 0.8808 (t0) cc_final: 0.8502 (t0) REVERT: D 21 ARG cc_start: 0.8965 (ttt90) cc_final: 0.8651 (ttt-90) REVERT: D 49 ARG cc_start: 0.7933 (mmt-90) cc_final: 0.6482 (mmt-90) REVERT: D 58 GLU cc_start: 0.9137 (pm20) cc_final: 0.8814 (pm20) REVERT: D 77 ASP cc_start: 0.8439 (t0) cc_final: 0.8071 (t0) REVERT: D 80 ASN cc_start: 0.9110 (m-40) cc_final: 0.8878 (m110) REVERT: D 89 ASN cc_start: 0.8812 (t0) cc_final: 0.8495 (t0) REVERT: D 104 GLU cc_start: 0.9330 (tt0) cc_final: 0.9090 (tt0) REVERT: F 49 ARG cc_start: 0.7919 (mmt-90) cc_final: 0.6457 (mmt-90) REVERT: F 58 GLU cc_start: 0.9149 (pm20) cc_final: 0.8829 (pm20) REVERT: F 77 ASP cc_start: 0.8442 (t0) cc_final: 0.8074 (t0) REVERT: F 80 ASN cc_start: 0.9111 (m-40) cc_final: 0.8879 (m110) REVERT: F 89 ASN cc_start: 0.8809 (t0) cc_final: 0.8494 (t0) REVERT: F 104 GLU cc_start: 0.9331 (tt0) cc_final: 0.9095 (tt0) REVERT: H 49 ARG cc_start: 0.7932 (mmt-90) cc_final: 0.6474 (mmt-90) REVERT: H 58 GLU cc_start: 0.9140 (pm20) cc_final: 0.8819 (pm20) REVERT: H 77 ASP cc_start: 0.8417 (t0) cc_final: 0.8061 (t0) REVERT: H 89 ASN cc_start: 0.8801 (t0) cc_final: 0.8490 (t0) REVERT: H 104 GLU cc_start: 0.9345 (tt0) cc_final: 0.9120 (tt0) REVERT: J 58 GLU cc_start: 0.9143 (pm20) cc_final: 0.8821 (pm20) REVERT: J 77 ASP cc_start: 0.8429 (t0) cc_final: 0.8060 (t0) REVERT: J 80 ASN cc_start: 0.9107 (m-40) cc_final: 0.8877 (m110) REVERT: J 89 ASN cc_start: 0.8812 (t0) cc_final: 0.8494 (t0) REVERT: J 104 GLU cc_start: 0.9334 (tt0) cc_final: 0.9097 (tt0) REVERT: L 58 GLU cc_start: 0.9142 (pm20) cc_final: 0.8826 (pm20) REVERT: L 77 ASP cc_start: 0.8428 (t0) cc_final: 0.8060 (t0) REVERT: L 80 ASN cc_start: 0.9109 (m-40) cc_final: 0.8879 (m110) REVERT: L 89 ASN cc_start: 0.8811 (t0) cc_final: 0.8493 (t0) REVERT: L 104 GLU cc_start: 0.9331 (tt0) cc_final: 0.9093 (tt0) REVERT: N 58 GLU cc_start: 0.9137 (pm20) cc_final: 0.8811 (pm20) REVERT: N 77 ASP cc_start: 0.8392 (t0) cc_final: 0.8004 (t0) REVERT: N 80 ASN cc_start: 0.9101 (m-40) cc_final: 0.8873 (m110) REVERT: N 89 ASN cc_start: 0.8799 (t0) cc_final: 0.8490 (t0) REVERT: P 58 GLU cc_start: 0.9142 (pm20) cc_final: 0.8819 (pm20) REVERT: P 77 ASP cc_start: 0.8420 (t0) cc_final: 0.8029 (t0) REVERT: P 80 ASN cc_start: 0.9103 (m-40) cc_final: 0.8874 (m110) REVERT: P 89 ASN cc_start: 0.8800 (t0) cc_final: 0.8493 (t0) REVERT: P 104 GLU cc_start: 0.9335 (tt0) cc_final: 0.9105 (tt0) outliers start: 34 outliers final: 19 residues processed: 504 average time/residue: 1.5191 time to fit residues: 858.7886 Evaluate side-chains 505 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 486 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 G residue 79 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 14 optimal weight: 0.9980 chunk 277 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.062001 restraints weight = 28936.081| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 1.87 r_work: 0.2532 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23120 Z= 0.174 Angle : 0.562 6.976 31232 Z= 0.302 Chirality : 0.041 0.119 3448 Planarity : 0.004 0.029 3912 Dihedral : 13.782 151.648 3896 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.69 % Favored : 98.03 % Rotamer: Outliers : 1.19 % Allowed : 15.01 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.16), residues: 2896 helix: 2.33 (0.14), residues: 1448 sheet: 0.93 (0.25), residues: 448 loop : -0.45 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 14 HIS 0.003 0.001 HIS K 124 PHE 0.012 0.001 PHE K 208 TYR 0.010 0.001 TYR P 42 ARG 0.004 0.001 ARG G 238 Details of bonding type rmsd hydrogen bonds : bond 0.05979 ( 1433) hydrogen bonds : angle 5.22106 ( 4107) SS BOND : bond 0.00033 ( 8) SS BOND : angle 0.50068 ( 16) covalent geometry : bond 0.00404 (23112) covalent geometry : angle 0.56179 (31216) *********************** 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 522 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 496 time to evaluate : 2.223 Fit side-chains REVERT: B 49 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.6509 (mmt-90) REVERT: B 58 GLU cc_start: 0.9143 (pm20) cc_final: 0.8792 (pm20) REVERT: B 77 ASP cc_start: 0.8449 (t0) cc_final: 0.8080 (t0) REVERT: B 80 ASN cc_start: 0.9114 (m-40) cc_final: 0.8866 (m110) REVERT: B 89 ASN cc_start: 0.8792 (t0) cc_final: 0.8472 (t0) REVERT: D 49 ARG cc_start: 0.7961 (mmt-90) cc_final: 0.6513 (mmt-90) REVERT: D 58 GLU cc_start: 0.9141 (pm20) cc_final: 0.8787 (pm20) REVERT: D 77 ASP cc_start: 0.8468 (t0) cc_final: 0.8099 (t0) REVERT: D 80 ASN cc_start: 0.9113 (m-40) cc_final: 0.8873 (m110) REVERT: D 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8479 (t0) REVERT: F 49 ARG cc_start: 0.7960 (mmt-90) cc_final: 0.6508 (mmt-90) REVERT: F 58 GLU cc_start: 0.9143 (pm20) cc_final: 0.8792 (pm20) REVERT: F 77 ASP cc_start: 0.8466 (t0) cc_final: 0.8096 (t0) REVERT: F 80 ASN cc_start: 0.9113 (m-40) cc_final: 0.8872 (m110) REVERT: F 89 ASN cc_start: 0.8784 (t0) cc_final: 0.8470 (t0) REVERT: H 49 ARG cc_start: 0.7963 (mmt-90) cc_final: 0.6512 (mmt-90) REVERT: H 58 GLU cc_start: 0.9135 (pm20) cc_final: 0.8785 (pm20) REVERT: H 77 ASP cc_start: 0.8451 (t0) cc_final: 0.8047 (t0) REVERT: H 80 ASN cc_start: 0.9110 (m-40) cc_final: 0.8839 (m110) REVERT: H 89 ASN cc_start: 0.8783 (t0) cc_final: 0.8459 (t0) REVERT: H 104 GLU cc_start: 0.9335 (tt0) cc_final: 0.9104 (tt0) REVERT: J 58 GLU cc_start: 0.9147 (pm20) cc_final: 0.8795 (pm20) REVERT: J 77 ASP cc_start: 0.8461 (t0) cc_final: 0.8090 (t0) REVERT: J 80 ASN cc_start: 0.9112 (m-40) cc_final: 0.8869 (m110) REVERT: J 89 ASN cc_start: 0.8791 (t0) cc_final: 0.8476 (t0) REVERT: L 58 GLU cc_start: 0.9143 (pm20) cc_final: 0.8797 (pm20) REVERT: L 77 ASP cc_start: 0.8460 (t0) cc_final: 0.8090 (t0) REVERT: L 80 ASN cc_start: 0.9111 (m-40) cc_final: 0.8870 (m110) REVERT: L 89 ASN cc_start: 0.8790 (t0) cc_final: 0.8473 (t0) REVERT: N 58 GLU cc_start: 0.9137 (pm20) cc_final: 0.8784 (pm20) REVERT: N 77 ASP cc_start: 0.8434 (t0) cc_final: 0.8064 (t0) REVERT: N 80 ASN cc_start: 0.9109 (m-40) cc_final: 0.8865 (m110) REVERT: N 89 ASN cc_start: 0.8786 (t0) cc_final: 0.8465 (t0) REVERT: P 58 GLU cc_start: 0.9142 (pm20) cc_final: 0.8790 (pm20) REVERT: P 77 ASP cc_start: 0.8453 (t0) cc_final: 0.8079 (t0) REVERT: P 80 ASN cc_start: 0.9105 (m-40) cc_final: 0.8863 (m110) REVERT: P 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8467 (t0) REVERT: P 104 GLU cc_start: 0.9320 (tt0) cc_final: 0.9080 (tt0) outliers start: 26 outliers final: 18 residues processed: 506 average time/residue: 1.5285 time to fit residues: 866.1984 Evaluate side-chains 506 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 488 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 224 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 244 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 266 optimal weight: 0.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.065109 restraints weight = 28802.600| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.86 r_work: 0.2600 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23120 Z= 0.109 Angle : 0.514 6.426 31232 Z= 0.273 Chirality : 0.038 0.117 3448 Planarity : 0.004 0.026 3912 Dihedral : 13.191 152.109 3896 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.80 % Favored : 97.93 % Rotamer: Outliers : 1.09 % Allowed : 14.51 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.16), residues: 2896 helix: 2.54 (0.14), residues: 1448 sheet: 0.89 (0.25), residues: 448 loop : -0.36 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.001 0.000 HIS M 124 PHE 0.010 0.001 PHE K 196 TYR 0.008 0.001 TYR C 223 ARG 0.007 0.001 ARG L 49 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 1433) hydrogen bonds : angle 4.95822 ( 4107) SS BOND : bond 0.00019 ( 8) SS BOND : angle 0.33296 ( 16) covalent geometry : bond 0.00221 (23112) covalent geometry : angle 0.51366 (31216) *********************** 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: 24 poor density : 497 time to evaluate : 2.168 Fit side-chains REVERT: B 49 ARG cc_start: 0.7904 (mmt-90) cc_final: 0.6392 (mmt-90) REVERT: B 58 GLU cc_start: 0.9177 (pm20) cc_final: 0.8851 (pm20) REVERT: B 89 ASN cc_start: 0.8796 (t0) cc_final: 0.8461 (t0) REVERT: D 21 ARG cc_start: 0.9004 (ttt90) cc_final: 0.8646 (ttt-90) REVERT: D 49 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.6403 (mmt-90) REVERT: D 58 GLU cc_start: 0.9179 (pm20) cc_final: 0.8850 (pm20) REVERT: D 89 ASN cc_start: 0.8805 (t0) cc_final: 0.8460 (t0) REVERT: F 49 ARG cc_start: 0.7905 (mmt-90) cc_final: 0.6392 (mmt-90) REVERT: F 58 GLU cc_start: 0.9178 (pm20) cc_final: 0.8854 (pm20) REVERT: F 89 ASN cc_start: 0.8796 (t0) cc_final: 0.8451 (t0) REVERT: H 49 ARG cc_start: 0.7910 (mmt-90) cc_final: 0.6403 (mmt-90) REVERT: H 58 GLU cc_start: 0.9174 (pm20) cc_final: 0.8848 (pm20) REVERT: H 77 ASP cc_start: 0.8409 (t0) cc_final: 0.8055 (t0) REVERT: H 80 ASN cc_start: 0.9064 (m-40) cc_final: 0.8819 (m110) REVERT: H 89 ASN cc_start: 0.8783 (t0) cc_final: 0.8442 (t0) REVERT: H 104 GLU cc_start: 0.9350 (tt0) cc_final: 0.9133 (tt0) REVERT: J 58 GLU cc_start: 0.9181 (pm20) cc_final: 0.8854 (pm20) REVERT: J 77 ASP cc_start: 0.8409 (t0) cc_final: 0.8026 (t0) REVERT: J 80 ASN cc_start: 0.9066 (m-40) cc_final: 0.8796 (m110) REVERT: J 89 ASN cc_start: 0.8798 (t0) cc_final: 0.8453 (t0) REVERT: L 58 GLU cc_start: 0.9182 (pm20) cc_final: 0.8859 (pm20) REVERT: L 77 ASP cc_start: 0.8408 (t0) cc_final: 0.8026 (t0) REVERT: L 80 ASN cc_start: 0.9069 (m-40) cc_final: 0.8800 (m110) REVERT: L 89 ASN cc_start: 0.8797 (t0) cc_final: 0.8450 (t0) REVERT: L 104 GLU cc_start: 0.9345 (tt0) cc_final: 0.9111 (tt0) REVERT: N 58 GLU cc_start: 0.9179 (pm20) cc_final: 0.8849 (pm20) REVERT: N 89 ASN cc_start: 0.8789 (t0) cc_final: 0.8453 (t0) REVERT: P 58 GLU cc_start: 0.9184 (pm20) cc_final: 0.8855 (pm20) REVERT: P 77 ASP cc_start: 0.8416 (t0) cc_final: 0.8032 (t0) REVERT: P 80 ASN cc_start: 0.9071 (m-40) cc_final: 0.8802 (m110) REVERT: P 89 ASN cc_start: 0.8790 (t0) cc_final: 0.8442 (t0) REVERT: P 104 GLU cc_start: 0.9342 (tt0) cc_final: 0.9122 (tt0) outliers start: 24 outliers final: 11 residues processed: 507 average time/residue: 1.5399 time to fit residues: 872.6294 Evaluate side-chains 491 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 480 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 G residue 79 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 203 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 228 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN D 80 ASN F 80 ASN H 5 GLN N 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.062885 restraints weight = 28888.871| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 1.87 r_work: 0.2553 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23120 Z= 0.148 Angle : 0.553 7.574 31232 Z= 0.294 Chirality : 0.040 0.116 3448 Planarity : 0.004 0.025 3912 Dihedral : 13.151 152.061 3896 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.86 % Favored : 97.86 % Rotamer: Outliers : 1.19 % Allowed : 14.42 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 2896 helix: 2.44 (0.14), residues: 1448 sheet: 0.81 (0.25), residues: 448 loop : -0.41 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 14 HIS 0.003 0.001 HIS M 124 PHE 0.011 0.001 PHE M 196 TYR 0.010 0.001 TYR G 223 ARG 0.007 0.001 ARG P 49 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 1433) hydrogen bonds : angle 5.11517 ( 4107) SS BOND : bond 0.00034 ( 8) SS BOND : angle 0.40886 ( 16) covalent geometry : bond 0.00335 (23112) covalent geometry : angle 0.55318 (31216) *********************** 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 518 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 492 time to evaluate : 2.300 Fit side-chains REVERT: B 49 ARG cc_start: 0.7966 (mmt-90) cc_final: 0.6411 (mmt-90) REVERT: B 58 GLU cc_start: 0.9172 (pm20) cc_final: 0.8817 (pm20) REVERT: B 77 ASP cc_start: 0.8429 (t0) cc_final: 0.8076 (t0) REVERT: B 80 ASN cc_start: 0.9074 (m-40) cc_final: 0.8837 (m110) REVERT: B 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8439 (t0) REVERT: D 49 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.6419 (mmt-90) REVERT: D 58 GLU cc_start: 0.9166 (pm20) cc_final: 0.8808 (pm20) REVERT: D 77 ASP cc_start: 0.8436 (t0) cc_final: 0.8083 (t0) REVERT: D 80 ASN cc_start: 0.9064 (m-40) cc_final: 0.8828 (m110) REVERT: D 89 ASN cc_start: 0.8789 (t0) cc_final: 0.8448 (t0) REVERT: F 49 ARG cc_start: 0.7965 (mmt-90) cc_final: 0.6404 (mmt-90) REVERT: F 58 GLU cc_start: 0.9171 (pm20) cc_final: 0.8817 (pm20) REVERT: F 77 ASP cc_start: 0.8437 (t0) cc_final: 0.8085 (t0) REVERT: F 80 ASN cc_start: 0.9070 (m-40) cc_final: 0.8835 (m110) REVERT: F 89 ASN cc_start: 0.8771 (t0) cc_final: 0.8425 (t0) REVERT: H 49 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.6414 (mmt-90) REVERT: H 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8808 (pm20) REVERT: H 77 ASP cc_start: 0.8421 (t0) cc_final: 0.8062 (t0) REVERT: H 80 ASN cc_start: 0.9038 (m-40) cc_final: 0.8793 (m110) REVERT: H 89 ASN cc_start: 0.8766 (t0) cc_final: 0.8416 (t0) REVERT: H 104 GLU cc_start: 0.9339 (tt0) cc_final: 0.9117 (tt0) REVERT: J 58 GLU cc_start: 0.9167 (pm20) cc_final: 0.8783 (pm20) REVERT: J 77 ASP cc_start: 0.8435 (t0) cc_final: 0.8078 (t0) REVERT: J 80 ASN cc_start: 0.9048 (m-40) cc_final: 0.8803 (m110) REVERT: J 89 ASN cc_start: 0.8775 (t0) cc_final: 0.8429 (t0) REVERT: L 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8818 (pm20) REVERT: L 77 ASP cc_start: 0.8435 (t0) cc_final: 0.8050 (t0) REVERT: L 80 ASN cc_start: 0.9055 (m-40) cc_final: 0.8796 (m110) REVERT: L 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8442 (t0) REVERT: L 104 GLU cc_start: 0.9328 (tt0) cc_final: 0.9083 (tt0) REVERT: N 58 GLU cc_start: 0.9160 (pm20) cc_final: 0.8773 (pm20) REVERT: N 77 ASP cc_start: 0.8414 (t0) cc_final: 0.8056 (t0) REVERT: N 80 ASN cc_start: 0.9069 (m-40) cc_final: 0.8835 (m110) REVERT: N 89 ASN cc_start: 0.8778 (t0) cc_final: 0.8432 (t0) REVERT: P 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8811 (pm20) REVERT: P 77 ASP cc_start: 0.8436 (t0) cc_final: 0.8078 (t0) REVERT: P 80 ASN cc_start: 0.9050 (m-40) cc_final: 0.8806 (m110) REVERT: P 89 ASN cc_start: 0.8782 (t0) cc_final: 0.8438 (t0) REVERT: P 104 GLU cc_start: 0.9333 (tt0) cc_final: 0.9110 (tt0) outliers start: 26 outliers final: 18 residues processed: 502 average time/residue: 1.5216 time to fit residues: 858.7919 Evaluate side-chains 502 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 484 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 187 optimal weight: 0.0000 chunk 231 optimal weight: 0.1980 chunk 206 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN D 5 GLN F 5 GLN H 5 GLN J 5 GLN L 5 GLN N 5 GLN P 5 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.063750 restraints weight = 28873.979| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 1.87 r_work: 0.2570 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1172 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= 0.130 Angle : 0.541 8.021 31232 Z= 0.286 Chirality : 0.039 0.117 3448 Planarity : 0.004 0.025 3912 Dihedral : 13.016 152.283 3896 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.19 % Allowed : 15.28 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.16), residues: 2896 helix: 2.48 (0.14), residues: 1448 sheet: 0.79 (0.25), residues: 448 loop : -0.38 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 14 HIS 0.002 0.001 HIS I 124 PHE 0.011 0.001 PHE K 208 TYR 0.009 0.001 TYR C 223 ARG 0.006 0.001 ARG L 49 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 1433) hydrogen bonds : angle 5.05456 ( 4107) SS BOND : bond 0.00009 ( 8) SS BOND : angle 0.36557 ( 16) covalent geometry : bond 0.00287 (23112) covalent geometry : angle 0.54129 (31216) *********************** 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 516 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 490 time to evaluate : 2.535 Fit side-chains REVERT: B 49 ARG cc_start: 0.7961 (mmt-90) cc_final: 0.6494 (mmt-90) REVERT: B 58 GLU cc_start: 0.9171 (pm20) cc_final: 0.8787 (pm20) REVERT: B 77 ASP cc_start: 0.8418 (t0) cc_final: 0.8036 (t0) REVERT: B 80 ASN cc_start: 0.9055 (m-40) cc_final: 0.8813 (m110) REVERT: B 89 ASN cc_start: 0.8782 (t0) cc_final: 0.8442 (t0) REVERT: D 49 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.6506 (mmt-90) REVERT: D 58 GLU cc_start: 0.9167 (pm20) cc_final: 0.8784 (pm20) REVERT: D 89 ASN cc_start: 0.8790 (t0) cc_final: 0.8463 (t0) REVERT: F 49 ARG cc_start: 0.7970 (mmt-90) cc_final: 0.6501 (mmt-90) REVERT: F 58 GLU cc_start: 0.9171 (pm20) cc_final: 0.8788 (pm20) REVERT: F 77 ASP cc_start: 0.8417 (t0) cc_final: 0.8037 (t0) REVERT: F 80 ASN cc_start: 0.9058 (m-40) cc_final: 0.8819 (m110) REVERT: F 89 ASN cc_start: 0.8777 (t0) cc_final: 0.8429 (t0) REVERT: H 49 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.6501 (mmt-90) REVERT: H 58 GLU cc_start: 0.9161 (pm20) cc_final: 0.8813 (pm20) REVERT: H 77 ASP cc_start: 0.8409 (t0) cc_final: 0.8055 (t0) REVERT: H 80 ASN cc_start: 0.9010 (m-40) cc_final: 0.8788 (m110) REVERT: H 89 ASN cc_start: 0.8767 (t0) cc_final: 0.8421 (t0) REVERT: H 104 GLU cc_start: 0.9346 (tt0) cc_final: 0.9127 (tt0) REVERT: J 58 GLU cc_start: 0.9173 (pm20) cc_final: 0.8792 (pm20) REVERT: J 77 ASP cc_start: 0.8424 (t0) cc_final: 0.8068 (t0) REVERT: J 80 ASN cc_start: 0.9020 (m-40) cc_final: 0.8786 (m110) REVERT: J 89 ASN cc_start: 0.8777 (t0) cc_final: 0.8428 (t0) REVERT: L 58 GLU cc_start: 0.9170 (pm20) cc_final: 0.8824 (pm20) REVERT: L 77 ASP cc_start: 0.8423 (t0) cc_final: 0.8066 (t0) REVERT: L 80 ASN cc_start: 0.9027 (m-40) cc_final: 0.8793 (m110) REVERT: L 89 ASN cc_start: 0.8782 (t0) cc_final: 0.8441 (t0) REVERT: L 104 GLU cc_start: 0.9338 (tt0) cc_final: 0.9097 (tt0) REVERT: N 58 GLU cc_start: 0.9167 (pm20) cc_final: 0.8780 (pm20) REVERT: N 89 ASN cc_start: 0.8778 (t0) cc_final: 0.8435 (t0) REVERT: P 58 GLU cc_start: 0.9171 (pm20) cc_final: 0.8787 (pm20) REVERT: P 77 ASP cc_start: 0.8422 (t0) cc_final: 0.8063 (t0) REVERT: P 80 ASN cc_start: 0.9020 (m-40) cc_final: 0.8784 (m110) REVERT: P 89 ASN cc_start: 0.8780 (t0) cc_final: 0.8451 (t0) REVERT: P 104 GLU cc_start: 0.9341 (tt0) cc_final: 0.9120 (tt0) outliers start: 26 outliers final: 18 residues processed: 500 average time/residue: 1.5145 time to fit residues: 846.9387 Evaluate side-chains 498 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 480 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 221 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN D 5 GLN D 80 ASN F 5 GLN H 5 GLN J 5 GLN L 5 GLN N 5 GLN N 80 ASN P 5 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.064203 restraints weight = 28859.463| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 1.86 r_work: 0.2579 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23120 Z= 0.126 Angle : 0.546 8.111 31232 Z= 0.289 Chirality : 0.039 0.117 3448 Planarity : 0.004 0.025 3912 Dihedral : 12.904 152.331 3896 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.19 % Allowed : 15.05 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.16), residues: 2896 helix: 2.50 (0.14), residues: 1448 sheet: 0.79 (0.25), residues: 448 loop : -0.37 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 14 HIS 0.002 0.001 HIS C 124 PHE 0.010 0.001 PHE M 208 TYR 0.009 0.001 TYR C 223 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 1433) hydrogen bonds : angle 5.02837 ( 4107) SS BOND : bond 0.00012 ( 8) SS BOND : angle 0.36494 ( 16) covalent geometry : bond 0.00277 (23112) covalent geometry : angle 0.54639 (31216) *********************** 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 527 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 501 time to evaluate : 2.340 Fit side-chains REVERT: B 49 ARG cc_start: 0.7983 (mmt-90) cc_final: 0.6506 (mmt-90) REVERT: B 58 GLU cc_start: 0.9156 (pm20) cc_final: 0.8777 (pm20) REVERT: B 89 ASN cc_start: 0.8780 (t0) cc_final: 0.8456 (t0) REVERT: D 49 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.6518 (mmt-90) REVERT: D 58 GLU cc_start: 0.9151 (pm20) cc_final: 0.8770 (pm20) REVERT: D 89 ASN cc_start: 0.8792 (t0) cc_final: 0.8472 (t0) REVERT: F 49 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.6512 (mmt-90) REVERT: F 58 GLU cc_start: 0.9151 (pm20) cc_final: 0.8771 (pm20) REVERT: F 89 ASN cc_start: 0.8771 (t0) cc_final: 0.8441 (t0) REVERT: H 49 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.6510 (mmt-90) REVERT: H 58 GLU cc_start: 0.9149 (pm20) cc_final: 0.8801 (pm20) REVERT: H 89 ASN cc_start: 0.8781 (t0) cc_final: 0.8452 (t0) REVERT: H 104 GLU cc_start: 0.9342 (tt0) cc_final: 0.9123 (tt0) REVERT: J 58 GLU cc_start: 0.9155 (pm20) cc_final: 0.8776 (pm20) REVERT: J 77 ASP cc_start: 0.8405 (t0) cc_final: 0.8046 (t0) REVERT: J 80 ASN cc_start: 0.9011 (m-40) cc_final: 0.8759 (m110) REVERT: J 89 ASN cc_start: 0.8770 (t0) cc_final: 0.8439 (t0) REVERT: L 58 GLU cc_start: 0.9157 (pm20) cc_final: 0.8810 (pm20) REVERT: L 77 ASP cc_start: 0.8407 (t0) cc_final: 0.8047 (t0) REVERT: L 80 ASN cc_start: 0.9025 (m-40) cc_final: 0.8777 (m110) REVERT: L 89 ASN cc_start: 0.8802 (t0) cc_final: 0.8478 (t0) REVERT: L 104 GLU cc_start: 0.9339 (tt0) cc_final: 0.9100 (tt0) REVERT: N 58 GLU cc_start: 0.9156 (pm20) cc_final: 0.8770 (pm20) REVERT: N 89 ASN cc_start: 0.8773 (t0) cc_final: 0.8449 (t0) REVERT: P 58 GLU cc_start: 0.9156 (pm20) cc_final: 0.8776 (pm20) REVERT: P 77 ASP cc_start: 0.8407 (t0) cc_final: 0.8048 (t0) REVERT: P 80 ASN cc_start: 0.9010 (m-40) cc_final: 0.8770 (m110) REVERT: P 89 ASN cc_start: 0.8776 (t0) cc_final: 0.8455 (t0) REVERT: P 104 GLU cc_start: 0.9338 (tt0) cc_final: 0.9118 (tt0) outliers start: 26 outliers final: 18 residues processed: 511 average time/residue: 1.5346 time to fit residues: 877.6887 Evaluate side-chains 507 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 489 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.8980 chunk 266 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 80 ASN D 5 GLN D 80 ASN F 5 GLN F 80 ASN H 5 GLN H 80 ASN J 5 GLN L 5 GLN N 5 GLN N 80 ASN P 5 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.062605 restraints weight = 28996.162| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 1.88 r_work: 0.2547 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23120 Z= 0.156 Angle : 0.566 8.241 31232 Z= 0.301 Chirality : 0.040 0.116 3448 Planarity : 0.004 0.025 3912 Dihedral : 13.078 152.322 3896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 0.82 % Allowed : 15.47 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.16), residues: 2896 helix: 2.39 (0.14), residues: 1448 sheet: 0.77 (0.25), residues: 448 loop : -0.42 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 14 HIS 0.003 0.001 HIS M 124 PHE 0.011 0.001 PHE G 208 TYR 0.010 0.001 TYR E 223 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.05584 ( 1433) hydrogen bonds : angle 5.15339 ( 4107) SS BOND : bond 0.00039 ( 8) SS BOND : angle 0.47574 ( 16) covalent geometry : bond 0.00358 (23112) covalent geometry : angle 0.56604 (31216) ********************** 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 511 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 493 time to evaluate : 2.217 Fit side-chains REVERT: B 49 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.6520 (mmt-90) REVERT: B 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8771 (pm20) REVERT: B 89 ASN cc_start: 0.8786 (t0) cc_final: 0.8464 (t0) REVERT: D 49 ARG cc_start: 0.8016 (mmt-90) cc_final: 0.6537 (mmt-90) REVERT: D 58 GLU cc_start: 0.9166 (pm20) cc_final: 0.8768 (pm20) REVERT: D 89 ASN cc_start: 0.8797 (t0) cc_final: 0.8476 (t0) REVERT: F 49 ARG cc_start: 0.8015 (mmt-90) cc_final: 0.6531 (mmt-90) REVERT: F 58 GLU cc_start: 0.9169 (pm20) cc_final: 0.8772 (pm20) REVERT: F 89 ASN cc_start: 0.8770 (t0) cc_final: 0.8439 (t0) REVERT: H 49 ARG cc_start: 0.8013 (mmt-90) cc_final: 0.6525 (mmt-90) REVERT: H 58 GLU cc_start: 0.9160 (pm20) cc_final: 0.8762 (pm20) REVERT: H 89 ASN cc_start: 0.8779 (t0) cc_final: 0.8449 (t0) REVERT: H 104 GLU cc_start: 0.9337 (tt0) cc_final: 0.9116 (tt0) REVERT: J 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8768 (pm20) REVERT: J 77 ASP cc_start: 0.8425 (t0) cc_final: 0.8063 (t0) REVERT: J 80 ASN cc_start: 0.9058 (m-40) cc_final: 0.8793 (m110) REVERT: J 89 ASN cc_start: 0.8775 (t0) cc_final: 0.8443 (t0) REVERT: L 58 GLU cc_start: 0.9162 (pm20) cc_final: 0.8771 (pm20) REVERT: L 77 ASP cc_start: 0.8421 (t0) cc_final: 0.8057 (t0) REVERT: L 80 ASN cc_start: 0.9059 (m-40) cc_final: 0.8791 (m110) REVERT: L 89 ASN cc_start: 0.8788 (t0) cc_final: 0.8464 (t0) REVERT: L 104 GLU cc_start: 0.9325 (tt0) cc_final: 0.9083 (tt0) REVERT: N 58 GLU cc_start: 0.9158 (pm20) cc_final: 0.8758 (pm20) REVERT: N 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8461 (t0) REVERT: P 58 GLU cc_start: 0.9165 (pm20) cc_final: 0.8768 (pm20) REVERT: P 77 ASP cc_start: 0.8419 (t0) cc_final: 0.8057 (t0) REVERT: P 80 ASN cc_start: 0.9056 (m-40) cc_final: 0.8803 (m110) REVERT: P 89 ASN cc_start: 0.8788 (t0) cc_final: 0.8465 (t0) REVERT: P 104 GLU cc_start: 0.9332 (tt0) cc_final: 0.9108 (tt0) outliers start: 18 outliers final: 18 residues processed: 503 average time/residue: 1.5849 time to fit residues: 891.7492 Evaluate side-chains 503 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 485 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 84 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 160 optimal weight: 2.9990 chunk 287 optimal weight: 0.0040 chunk 138 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 80 ASN D 5 GLN D 80 ASN F 5 GLN F 80 ASN H 5 GLN H 80 ASN J 5 GLN L 5 GLN N 5 GLN N 80 ASN P 5 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.064748 restraints weight = 28579.770| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 1.85 r_work: 0.2591 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23120 Z= 0.122 Angle : 0.548 8.368 31232 Z= 0.289 Chirality : 0.039 0.116 3448 Planarity : 0.004 0.025 3912 Dihedral : 12.817 152.570 3896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.80 % Favored : 97.93 % Rotamer: Outliers : 1.19 % Allowed : 15.28 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.16), residues: 2896 helix: 2.40 (0.14), residues: 1496 sheet: 0.77 (0.25), residues: 448 loop : -0.33 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.002 0.001 HIS I 124 PHE 0.011 0.001 PHE O 208 TYR 0.009 0.001 TYR E 223 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 1433) hydrogen bonds : angle 4.99367 ( 4107) SS BOND : bond 0.00003 ( 8) SS BOND : angle 0.35789 ( 16) covalent geometry : bond 0.00263 (23112) covalent geometry : angle 0.54803 (31216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25102.62 seconds wall clock time: 431 minutes 32.53 seconds (25892.53 seconds total)