Starting phenix.real_space_refine on Sun Mar 17 06:53:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/03_2024/7zxo_15012.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/03_2024/7zxo_15012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/03_2024/7zxo_15012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/03_2024/7zxo_15012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/03_2024/7zxo_15012.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/03_2024/7zxo_15012.pdb" } resolution = 2.5 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 11328 2.51 5 N 2712 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "I TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 146": "OE1" <-> "OE2" Residue "J TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 146": "OE1" <-> "OE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "L TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 146": "OE1" <-> "OE2" Residue "L TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 186": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17016 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "B" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "C" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "F" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "G" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "H" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "I" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "J" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "K" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "L" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1418 Classifications: {'peptide': 177} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Time building chain proxies: 8.70, per 1000 atoms: 0.51 Number of scatterers: 17016 At special positions: 0 Unit cell: (103.986, 93.522, 153.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 2820 8.00 N 2712 7.00 C 11328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 6.52 Conformation dependent library (CDL) restraints added in 2.9 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 74.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 103 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 157 Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 103 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 157 Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 103 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 157 Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG D 22 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 103 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 157 Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 103 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 157 Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG F 22 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 103 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 157 Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 103 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 157 Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 103 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 157 Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 103 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 157 Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG J 22 " --> pdb=" O THR J 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 103 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 157 Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG K 22 " --> pdb=" O THR K 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 103 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 157 Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 18 through 43 removed outlier: 4.133A pdb=" N ARG L 22 " --> pdb=" O THR L 18 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 103 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 157 Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.933A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.932A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5052 1.35 - 1.46: 4516 1.46 - 1.58: 7712 1.58 - 1.70: 0 1.70 - 1.81: 216 Bond restraints: 17496 Sorted by residual: bond pdb=" CB PRO B 87 " pdb=" CG PRO B 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO H 87 " pdb=" CG PRO H 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO E 87 " pdb=" CG PRO E 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO F 87 " pdb=" CG PRO F 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CB PRO C 87 " pdb=" CG PRO C 87 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 ... (remaining 17491 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 636 107.28 - 113.96: 10065 113.96 - 120.65: 7128 120.65 - 127.33: 5832 127.33 - 134.01: 243 Bond angle restraints: 23904 Sorted by residual: angle pdb=" CA PRO D 87 " pdb=" N PRO D 87 " pdb=" CD PRO D 87 " ideal model delta sigma weight residual 112.00 104.89 7.11 1.40e+00 5.10e-01 2.58e+01 angle pdb=" CA PRO K 87 " pdb=" N PRO K 87 " pdb=" CD PRO K 87 " ideal model delta sigma weight residual 112.00 104.90 7.10 1.40e+00 5.10e-01 2.57e+01 angle pdb=" CA PRO E 87 " pdb=" N PRO E 87 " pdb=" CD PRO E 87 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CA PRO J 87 " pdb=" N PRO J 87 " pdb=" CD PRO J 87 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CA PRO B 87 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 112.00 104.93 7.07 1.40e+00 5.10e-01 2.55e+01 ... (remaining 23899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 8328 11.94 - 23.87: 1080 23.87 - 35.81: 540 35.81 - 47.74: 120 47.74 - 59.68: 120 Dihedral angle restraints: 10188 sinusoidal: 3888 harmonic: 6300 Sorted by residual: dihedral pdb=" CB CYS J 60 " pdb=" SG CYS J 60 " pdb=" SG CYS J 173 " pdb=" CB CYS J 173 " ideal model delta sinusoidal sigma weight residual 93.00 126.64 -33.64 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CB CYS D 60 " pdb=" SG CYS D 60 " pdb=" SG CYS D 173 " pdb=" CB CYS D 173 " ideal model delta sinusoidal sigma weight residual 93.00 126.62 -33.62 1 1.00e+01 1.00e-02 1.61e+01 dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 173 " pdb=" CB CYS B 173 " ideal model delta sinusoidal sigma weight residual 93.00 126.62 -33.62 1 1.00e+01 1.00e-02 1.61e+01 ... (remaining 10185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2018 0.035 - 0.070: 607 0.070 - 0.105: 187 0.105 - 0.140: 20 0.140 - 0.175: 24 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA THR E 86 " pdb=" N THR E 86 " pdb=" C THR E 86 " pdb=" CB THR E 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA THR D 86 " pdb=" N THR D 86 " pdb=" C THR D 86 " pdb=" CB THR D 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA THR L 86 " pdb=" N THR L 86 " pdb=" C THR L 86 " pdb=" CB THR L 86 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 2853 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 86 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO K 87 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO K 87 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO K 87 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 86 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO D 87 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 86 " 0.080 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 87 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 87 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 87 " 0.064 5.00e-02 4.00e+02 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1982 2.75 - 3.29: 17283 3.29 - 3.83: 31280 3.83 - 4.36: 31344 4.36 - 4.90: 56891 Nonbonded interactions: 138780 Sorted by model distance: nonbonded pdb=" O ARG G 22 " pdb=" OG SER G 26 " model vdw 2.216 2.440 nonbonded pdb=" O ARG A 22 " pdb=" OG SER A 26 " model vdw 2.216 2.440 nonbonded pdb=" O ARG E 22 " pdb=" OG SER E 26 " model vdw 2.217 2.440 nonbonded pdb=" O ARG K 22 " pdb=" OG SER K 26 " model vdw 2.217 2.440 nonbonded pdb=" O ARG J 22 " pdb=" OG SER J 26 " model vdw 2.217 2.440 ... (remaining 138775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.500 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.430 Find NCS groups from input model: 1.190 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: 0.010 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 0.086 17496 Z= 0.214 Angle : 0.523 7.112 23904 Z= 0.305 Chirality : 0.040 0.175 2856 Planarity : 0.008 0.117 2856 Dihedral : 15.391 59.678 5976 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.36 % Allowed : 19.39 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.19 (0.16), residues: 2076 helix: 4.15 (0.10), residues: 1500 sheet: 1.48 (0.48), residues: 132 loop : -2.28 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.002 0.001 HIS K 94 PHE 0.011 0.001 PHE I 180 TYR 0.008 0.001 TYR J 65 ARG 0.001 0.000 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 298 time to evaluate : 1.949 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 322 average time/residue: 1.0592 time to fit residues: 385.5666 Evaluate side-chains 248 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17496 Z= 0.226 Angle : 0.496 5.107 23904 Z= 0.269 Chirality : 0.041 0.163 2856 Planarity : 0.006 0.078 2856 Dihedral : 4.008 14.963 2292 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.35 % Allowed : 18.61 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.11 (0.16), residues: 2076 helix: 4.07 (0.10), residues: 1488 sheet: 1.62 (0.49), residues: 132 loop : -2.09 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.002 0.001 HIS H 97 PHE 0.015 0.002 PHE B 180 TYR 0.012 0.001 TYR J 65 ARG 0.002 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 248 time to evaluate : 1.854 Fit side-chains REVERT: A 93 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7387 (mpp) REVERT: D 93 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7387 (mpp) REVERT: G 93 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7387 (mpp) REVERT: J 93 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7383 (mpp) outliers start: 83 outliers final: 23 residues processed: 295 average time/residue: 1.0644 time to fit residues: 356.2367 Evaluate side-chains 256 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17496 Z= 0.310 Angle : 0.518 5.548 23904 Z= 0.281 Chirality : 0.042 0.181 2856 Planarity : 0.005 0.062 2856 Dihedral : 3.939 15.279 2280 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.51 % Allowed : 18.61 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.85 (0.16), residues: 2076 helix: 3.85 (0.10), residues: 1488 sheet: 1.51 (0.48), residues: 132 loop : -2.06 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 132 HIS 0.003 0.001 HIS K 97 PHE 0.016 0.002 PHE B 180 TYR 0.015 0.002 TYR H 65 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 216 time to evaluate : 2.060 Fit side-chains REVERT: A 93 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7468 (mpp) REVERT: D 93 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7468 (mpp) REVERT: G 93 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7462 (mpp) REVERT: J 93 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7456 (mpp) outliers start: 67 outliers final: 21 residues processed: 275 average time/residue: 1.1216 time to fit residues: 348.0898 Evaluate side-chains 241 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17496 Z= 0.252 Angle : 0.484 5.235 23904 Z= 0.261 Chirality : 0.040 0.169 2856 Planarity : 0.004 0.052 2856 Dihedral : 3.864 15.387 2280 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.99 % Allowed : 19.39 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.96 (0.16), residues: 2076 helix: 3.95 (0.10), residues: 1488 sheet: 1.50 (0.48), residues: 132 loop : -2.08 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 132 HIS 0.004 0.001 HIS H 97 PHE 0.014 0.002 PHE E 180 TYR 0.013 0.002 TYR H 65 ARG 0.002 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 216 time to evaluate : 1.688 Fit side-chains REVERT: A 93 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7442 (mpp) REVERT: D 93 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7439 (mpp) REVERT: G 93 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7436 (mpp) REVERT: J 93 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7438 (mpp) outliers start: 57 outliers final: 29 residues processed: 260 average time/residue: 1.2445 time to fit residues: 360.3233 Evaluate side-chains 249 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17496 Z= 0.210 Angle : 0.463 5.190 23904 Z= 0.248 Chirality : 0.039 0.162 2856 Planarity : 0.004 0.045 2856 Dihedral : 3.737 15.181 2280 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.73 % Allowed : 20.65 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.18 (0.16), residues: 2076 helix: 4.12 (0.10), residues: 1488 sheet: 1.57 (0.48), residues: 132 loop : -2.04 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 132 HIS 0.002 0.001 HIS I 97 PHE 0.013 0.002 PHE J 180 TYR 0.011 0.001 TYR J 65 ARG 0.002 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 220 time to evaluate : 2.034 Fit side-chains outliers start: 52 outliers final: 24 residues processed: 260 average time/residue: 1.2495 time to fit residues: 362.7714 Evaluate side-chains 240 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 216 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 98 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 98 GLN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS G 98 GLN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 97 HIS J 98 GLN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17496 Z= 0.160 Angle : 0.447 4.912 23904 Z= 0.239 Chirality : 0.038 0.150 2856 Planarity : 0.003 0.042 2856 Dihedral : 3.588 15.017 2280 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.36 % Allowed : 21.80 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.39 (0.17), residues: 2076 helix: 4.31 (0.10), residues: 1488 sheet: 1.79 (0.50), residues: 132 loop : -2.14 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 132 HIS 0.003 0.001 HIS C 97 PHE 0.010 0.001 PHE E 180 TYR 0.007 0.001 TYR A 65 ARG 0.002 0.000 ARG L 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 1.892 Fit side-chains outliers start: 45 outliers final: 20 residues processed: 274 average time/residue: 1.2142 time to fit residues: 371.4032 Evaluate side-chains 246 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 25 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17496 Z= 0.287 Angle : 0.502 5.183 23904 Z= 0.270 Chirality : 0.041 0.156 2856 Planarity : 0.004 0.040 2856 Dihedral : 3.723 14.865 2280 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.89 % Allowed : 22.54 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.07 (0.17), residues: 2076 helix: 4.03 (0.10), residues: 1488 sheet: 1.57 (0.49), residues: 132 loop : -2.05 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 133 HIS 0.006 0.001 HIS I 97 PHE 0.013 0.002 PHE K 180 TYR 0.016 0.002 TYR J 65 ARG 0.002 0.000 ARG I 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 222 time to evaluate : 1.919 Fit side-chains REVERT: B 156 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8902 (mp) REVERT: K 156 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8903 (mp) outliers start: 36 outliers final: 24 residues processed: 254 average time/residue: 1.3082 time to fit residues: 369.0199 Evaluate side-chains 244 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 156 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 25 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17496 Z= 0.203 Angle : 0.469 5.098 23904 Z= 0.251 Chirality : 0.039 0.150 2856 Planarity : 0.003 0.039 2856 Dihedral : 3.637 14.790 2280 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.52 % Allowed : 23.06 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.23 (0.17), residues: 2076 helix: 4.18 (0.10), residues: 1488 sheet: 1.58 (0.49), residues: 132 loop : -2.09 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 132 HIS 0.005 0.001 HIS C 97 PHE 0.012 0.002 PHE K 180 TYR 0.011 0.001 TYR J 65 ARG 0.001 0.000 ARG L 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 222 time to evaluate : 2.097 Fit side-chains outliers start: 29 outliers final: 25 residues processed: 249 average time/residue: 1.2960 time to fit residues: 358.3737 Evaluate side-chains 247 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 25 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17496 Z= 0.191 Angle : 0.478 5.071 23904 Z= 0.256 Chirality : 0.039 0.147 2856 Planarity : 0.003 0.038 2856 Dihedral : 3.572 14.672 2280 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.52 % Allowed : 23.74 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.28 (0.17), residues: 2076 helix: 4.22 (0.10), residues: 1488 sheet: 1.71 (0.50), residues: 132 loop : -2.11 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 132 HIS 0.007 0.001 HIS C 97 PHE 0.011 0.002 PHE H 180 TYR 0.010 0.001 TYR J 65 ARG 0.002 0.000 ARG L 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 230 time to evaluate : 2.094 Fit side-chains outliers start: 29 outliers final: 25 residues processed: 257 average time/residue: 1.2873 time to fit residues: 368.0196 Evaluate side-chains 247 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17496 Z= 0.169 Angle : 0.470 5.099 23904 Z= 0.251 Chirality : 0.038 0.145 2856 Planarity : 0.003 0.037 2856 Dihedral : 3.503 14.655 2280 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.31 % Allowed : 23.95 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.40 (0.17), residues: 2076 helix: 4.32 (0.10), residues: 1488 sheet: 1.79 (0.51), residues: 132 loop : -2.16 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 132 HIS 0.004 0.001 HIS F 97 PHE 0.010 0.001 PHE B 180 TYR 0.008 0.001 TYR A 65 ARG 0.002 0.000 ARG F 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 1.858 Fit side-chains outliers start: 25 outliers final: 20 residues processed: 252 average time/residue: 1.3068 time to fit residues: 365.2948 Evaluate side-chains 243 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 166 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.077764 restraints weight = 25776.811| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.99 r_work: 0.2870 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17496 Z= 0.153 Angle : 0.466 5.348 23904 Z= 0.248 Chirality : 0.038 0.141 2856 Planarity : 0.003 0.037 2856 Dihedral : 3.386 14.455 2280 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.47 % Allowed : 23.53 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.55 (0.17), residues: 2076 helix: 4.44 (0.10), residues: 1488 sheet: 1.95 (0.52), residues: 132 loop : -2.17 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 132 HIS 0.003 0.001 HIS I 97 PHE 0.008 0.001 PHE C 180 TYR 0.016 0.001 TYR K 171 ARG 0.003 0.000 ARG L 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6076.41 seconds wall clock time: 108 minutes 1.57 seconds (6481.57 seconds total)