Starting phenix.real_space_refine on Sat Jan 25 16:11:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy6_42793/01_2025/8uy6_42793_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy6_42793/01_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_42793/01_2025/8uy6_42793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy6_42793/01_2025/8uy6_42793.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy6_42793/01_2025/8uy6_42793_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy6_42793/01_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 13.35, per 1000 atoms: 0.59 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: 6.04 Conformation dependent library (CDL) restraints added in 2.9 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: 2.80 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: 7.45 Time building geometry restraints manager: 6.84 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 49.490 Find NCS groups from input model: 0.440 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.690 ------------------------------------------------------------------------------- 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 23112 Z= 0.175 Angle : 0.533 8.477 31216 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 *********************** 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 : 2.125 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 534 average time/residue: 1.6719 time to fit residues: 994.2648 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 : 2.203 ------------------------------------------------------------------------------- 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 23112 Z= 0.149 Angle : 0.515 4.691 31216 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 *********************** 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 : 2.284 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: 1.7613 time to fit residues: 1009.1807 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 : 2.476 ------------------------------------------------------------------------------- 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 23112 Z= 0.259 Angle : 0.550 6.690 31216 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 *********************** 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 : 2.449 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: 1.6208 time to fit residues: 922.1741 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 : 3.148 ------------------------------------------------------------------------------- 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 23112 Z= 0.224 Angle : 0.538 6.800 31216 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 *********************** 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 : 2.418 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: 1.6167 time to fit residues: 910.0910 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 : 2.280 ------------------------------------------------------------------------------- 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 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 23112 Z= 0.267 Angle : 0.562 6.976 31216 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 *********************** 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 : 2.327 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: 1.5989 time to fit residues: 904.9636 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 : 2.475 ------------------------------------------------------------------------------- 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 23112 Z= 0.147 Angle : 0.514 6.426 31216 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 *********************** 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 : 2.434 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: 1.6282 time to fit residues: 921.6296 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 : 2.365 ------------------------------------------------------------------------------- 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 23112 Z= 0.221 Angle : 0.553 7.574 31216 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 *********************** 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 : 2.278 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: 1.6486 time to fit residues: 926.0498 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 : 2.265 ------------------------------------------------------------------------------- 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 23112 Z= 0.190 Angle : 0.541 8.021 31216 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 *********************** 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 : 2.365 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: 1.6388 time to fit residues: 914.8157 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 : 2.487 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 0.8980 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: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.093842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.063562 restraints weight = 28872.325| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 1.87 r_work: 0.2567 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23112 Z= 0.198 Angle : 0.553 8.127 31216 Z= 0.293 Chirality : 0.039 0.117 3448 Planarity : 0.004 0.025 3912 Dihedral : 12.971 152.319 3896 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.46 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: 1.87 (0.16), residues: 2896 helix: 2.46 (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 E 14 HIS 0.002 0.001 HIS C 124 PHE 0.010 0.001 PHE O 208 TYR 0.010 0.001 TYR K 223 ARG 0.006 0.001 ARG O 238 *********************** 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 520 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 494 time to evaluate : 2.348 Fit side-chains REVERT: B 49 ARG cc_start: 0.7981 (mmt-90) cc_final: 0.6503 (mmt-90) REVERT: B 58 GLU cc_start: 0.9161 (pm20) cc_final: 0.8775 (pm20) REVERT: B 89 ASN cc_start: 0.8784 (t0) cc_final: 0.8459 (t0) REVERT: D 49 ARG cc_start: 0.7999 (mmt-90) cc_final: 0.6528 (mmt-90) REVERT: D 58 GLU cc_start: 0.9156 (pm20) cc_final: 0.8769 (pm20) REVERT: D 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8474 (t0) REVERT: F 49 ARG cc_start: 0.7997 (mmt-90) cc_final: 0.6521 (mmt-90) REVERT: F 58 GLU cc_start: 0.9161 (pm20) cc_final: 0.8776 (pm20) REVERT: F 89 ASN cc_start: 0.8772 (t0) cc_final: 0.8442 (t0) REVERT: H 49 ARG cc_start: 0.7995 (mmt-90) cc_final: 0.6516 (mmt-90) REVERT: H 58 GLU cc_start: 0.9161 (pm20) cc_final: 0.8812 (pm20) REVERT: H 89 ASN cc_start: 0.8767 (t0) cc_final: 0.8438 (t0) REVERT: H 104 GLU cc_start: 0.9343 (tt0) cc_final: 0.9124 (tt0) REVERT: J 58 GLU cc_start: 0.9160 (pm20) cc_final: 0.8776 (pm20) REVERT: J 77 ASP cc_start: 0.8414 (t0) cc_final: 0.8056 (t0) REVERT: J 80 ASN cc_start: 0.9018 (m-40) cc_final: 0.8768 (m110) REVERT: J 89 ASN cc_start: 0.8772 (t0) cc_final: 0.8442 (t0) REVERT: L 58 GLU cc_start: 0.9160 (pm20) cc_final: 0.8810 (pm20) REVERT: L 77 ASP cc_start: 0.8411 (t0) cc_final: 0.8053 (t0) REVERT: L 80 ASN cc_start: 0.9026 (m-40) cc_final: 0.8779 (m110) REVERT: L 89 ASN cc_start: 0.8783 (t0) cc_final: 0.8459 (t0) REVERT: L 104 GLU cc_start: 0.9332 (tt0) cc_final: 0.9093 (tt0) REVERT: N 58 GLU cc_start: 0.9156 (pm20) cc_final: 0.8766 (pm20) REVERT: N 89 ASN cc_start: 0.8774 (t0) cc_final: 0.8449 (t0) REVERT: P 58 GLU cc_start: 0.9161 (pm20) cc_final: 0.8775 (pm20) REVERT: P 77 ASP cc_start: 0.8407 (t0) cc_final: 0.8047 (t0) REVERT: P 80 ASN cc_start: 0.9018 (m-40) cc_final: 0.8767 (m110) REVERT: P 89 ASN cc_start: 0.8778 (t0) cc_final: 0.8456 (t0) REVERT: P 104 GLU cc_start: 0.9339 (tt0) cc_final: 0.9119 (tt0) outliers start: 26 outliers final: 22 residues processed: 504 average time/residue: 1.6554 time to fit residues: 934.4445 Evaluate side-chains 508 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 486 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain 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: 1.9990 chunk 266 optimal weight: 5.9990 chunk 273 optimal weight: 0.0010 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.093275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.062940 restraints weight = 28971.675| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 1.88 r_work: 0.2553 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23112 Z= 0.224 Angle : 0.564 8.225 31216 Z= 0.300 Chirality : 0.040 0.117 3448 Planarity : 0.004 0.025 3912 Dihedral : 13.054 152.391 3896 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % Rotamer: Outliers : 1.00 % Allowed : 15.24 % 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: 1.80 (0.16), residues: 2896 helix: 2.40 (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 0.011 0.001 TRP M 14 HIS 0.002 0.001 HIS I 124 PHE 0.011 0.001 PHE C 208 TYR 0.010 0.001 TYR C 223 ARG 0.006 0.001 ARG A 238 ********************** 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 517 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 495 time to evaluate : 2.425 Fit side-chains REVERT: B 49 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.6511 (mmt-90) REVERT: B 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8773 (pm20) REVERT: B 89 ASN cc_start: 0.8784 (t0) cc_final: 0.8463 (t0) REVERT: D 49 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.6525 (mmt-90) REVERT: D 58 GLU cc_start: 0.9166 (pm20) cc_final: 0.8772 (pm20) REVERT: D 89 ASN cc_start: 0.8791 (t0) cc_final: 0.8474 (t0) REVERT: F 49 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.6521 (mmt-90) REVERT: F 58 GLU cc_start: 0.9170 (pm20) cc_final: 0.8776 (pm20) REVERT: F 89 ASN cc_start: 0.8774 (t0) cc_final: 0.8447 (t0) REVERT: H 49 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.6519 (mmt-90) REVERT: H 58 GLU cc_start: 0.9159 (pm20) cc_final: 0.8767 (pm20) REVERT: H 89 ASN cc_start: 0.8778 (t0) cc_final: 0.8451 (t0) REVERT: H 104 GLU cc_start: 0.9336 (tt0) cc_final: 0.9115 (tt0) REVERT: J 58 GLU cc_start: 0.9164 (pm20) cc_final: 0.8773 (pm20) REVERT: J 77 ASP cc_start: 0.8423 (t0) cc_final: 0.8059 (t0) REVERT: J 80 ASN cc_start: 0.9050 (m-40) cc_final: 0.8779 (m110) REVERT: J 89 ASN cc_start: 0.8775 (t0) cc_final: 0.8448 (t0) REVERT: L 58 GLU cc_start: 0.9168 (pm20) cc_final: 0.8784 (pm20) REVERT: L 77 ASP cc_start: 0.8420 (t0) cc_final: 0.8057 (t0) REVERT: L 80 ASN cc_start: 0.9059 (m-40) cc_final: 0.8795 (m110) REVERT: L 89 ASN cc_start: 0.8786 (t0) cc_final: 0.8463 (t0) REVERT: N 58 GLU cc_start: 0.9158 (pm20) cc_final: 0.8759 (pm20) REVERT: N 89 ASN cc_start: 0.8784 (t0) cc_final: 0.8463 (t0) REVERT: P 58 GLU cc_start: 0.9170 (pm20) cc_final: 0.8776 (pm20) REVERT: P 77 ASP cc_start: 0.8416 (t0) cc_final: 0.8055 (t0) REVERT: P 80 ASN cc_start: 0.9048 (m-40) cc_final: 0.8795 (m110) REVERT: P 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8464 (t0) REVERT: P 104 GLU cc_start: 0.9332 (tt0) cc_final: 0.9109 (tt0) outliers start: 22 outliers final: 22 residues processed: 505 average time/residue: 1.6550 time to fit residues: 932.4594 Evaluate side-chains 509 residues out of total 2192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 487 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain 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: 5.9990 chunk 287 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 80 ASN D 5 GLN D 80 ASN F 5 GLN 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 = 0.3266 r_free = 0.3266 target = 0.093820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.063578 restraints weight = 28601.391| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.86 r_work: 0.2567 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23112 Z= 0.206 Angle : 0.561 8.446 31216 Z= 0.297 Chirality : 0.039 0.117 3448 Planarity : 0.004 0.025 3912 Dihedral : 12.963 152.570 3896 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.66 % Favored : 98.07 % 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: 1.84 (0.16), residues: 2896 helix: 2.45 (0.14), residues: 1448 sheet: 0.77 (0.25), residues: 448 loop : -0.40 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 14 HIS 0.002 0.001 HIS A 124 PHE 0.010 0.001 PHE I 208 TYR 0.009 0.001 TYR E 223 ARG 0.006 0.001 ARG A 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25202.80 seconds wall clock time: 447 minutes 51.18 seconds (26871.18 seconds total)