Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 15:28:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/07_2023/7zxo_15012.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/07_2023/7zxo_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_15012/07_2023/7zxo_15012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/07_2023/7zxo_15012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/07_2023/7zxo_15012.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxo_15012/07_2023/7zxo_15012.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 8.42, per 1000 atoms: 0.49 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: 7.14 Conformation dependent library (CDL) restraints added in 2.5 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: 0.57 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: 5.15 Time building geometry restraints manager: 7.67 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: 2.590 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: 13.160 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 43.480 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 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:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.200 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.976 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 322 average time/residue: 1.1411 time to fit residues: 415.1662 Evaluate side-chains 248 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 236 time to evaluate : 2.113 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.6895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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: 0.8489 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 17496 Z= 0.153 Angle : 0.454 4.815 23904 Z= 0.246 Chirality : 0.039 0.155 2856 Planarity : 0.006 0.079 2856 Dihedral : 3.814 15.000 2280 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.35 % 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: 4.32 (0.16), residues: 2076 helix: 4.26 (0.09), residues: 1488 sheet: 1.85 (0.50), residues: 132 loop : -2.21 (0.21), residues: 456 *********************** 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 312 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 248 time to evaluate : 2.128 Fit side-chains outliers start: 64 outliers final: 28 residues processed: 288 average time/residue: 1.1307 time to fit residues: 370.3006 Evaluate side-chains 264 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.6452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 200 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 0.8538 moved from start: 0.1608 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= 0.194 Angle : 0.464 5.333 23904 Z= 0.250 Chirality : 0.039 0.164 2856 Planarity : 0.005 0.066 2856 Dihedral : 3.799 15.291 2280 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 4.45 % 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: 4.20 (0.16), residues: 2076 helix: 4.16 (0.09), residues: 1488 sheet: 1.73 (0.49), residues: 132 loop : -2.19 (0.22), residues: 456 *********************** 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 313 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 228 time to evaluate : 2.007 Fit side-chains outliers start: 85 outliers final: 29 residues processed: 304 average time/residue: 1.0406 time to fit residues: 360.5160 Evaluate side-chains 257 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 228 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 0.1586 time to fit residues: 4.2653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.8543 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 17496 Z= 0.189 Angle : 0.450 5.111 23904 Z= 0.243 Chirality : 0.039 0.161 2856 Planarity : 0.004 0.053 2856 Dihedral : 3.705 14.478 2280 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 2.88 % 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: 4.28 (0.16), residues: 2076 helix: 4.25 (0.09), residues: 1488 sheet: 1.72 (0.49), residues: 132 loop : -2.27 (0.22), residues: 456 *********************** 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 278 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 223 time to evaluate : 2.188 Fit side-chains outliers start: 55 outliers final: 33 residues processed: 266 average time/residue: 1.1865 time to fit residues: 356.2137 Evaluate side-chains 256 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 223 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 0.1524 time to fit residues: 5.0732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 17496 Z= 0.362 Angle : 0.550 5.547 23904 Z= 0.294 Chirality : 0.043 0.178 2856 Planarity : 0.004 0.049 2856 Dihedral : 3.894 15.995 2280 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 3.83 % 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: 3.78 (0.16), residues: 2076 helix: 3.81 (0.10), residues: 1488 sheet: 1.48 (0.47), residues: 132 loop : -2.14 (0.23), residues: 456 *********************** 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 289 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 216 time to evaluate : 2.006 Fit side-chains outliers start: 73 outliers final: 41 residues processed: 277 average time/residue: 1.2199 time to fit residues: 379.8157 Evaluate side-chains 257 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 6 average time/residue: 0.1509 time to fit residues: 4.2816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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** ** 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: 0.8557 moved from start: 0.2356 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= 0.166 Angle : 0.456 5.015 23904 Z= 0.243 Chirality : 0.038 0.152 2856 Planarity : 0.004 0.044 2856 Dihedral : 3.697 14.997 2280 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 2.57 % 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: 4.20 (0.10), residues: 1488 sheet: 1.55 (0.48), residues: 132 loop : -2.14 (0.23), residues: 456 *********************** 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 278 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 2.138 Fit side-chains outliers start: 49 outliers final: 29 residues processed: 278 average time/residue: 1.2609 time to fit residues: 392.4982 Evaluate side-chains 250 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 2.112 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 2.7630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 17496 Z= 0.274 Angle : 0.498 5.082 23904 Z= 0.267 Chirality : 0.040 0.156 2856 Planarity : 0.004 0.042 2856 Dihedral : 3.726 14.670 2280 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 1.78 % 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: 4.01 (0.16), residues: 2076 helix: 4.00 (0.10), residues: 1488 sheet: 1.52 (0.48), residues: 132 loop : -2.12 (0.23), residues: 456 *********************** 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 259 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 2.105 Fit side-chains outliers start: 34 outliers final: 31 residues processed: 259 average time/residue: 1.3472 time to fit residues: 387.7535 Evaluate side-chains 250 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 219 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 2.6323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 0.0050 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 98 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 17496 Z= 0.169 Angle : 0.462 4.933 23904 Z= 0.247 Chirality : 0.038 0.149 2856 Planarity : 0.003 0.041 2856 Dihedral : 3.591 14.833 2280 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 2.88 % 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: 4.35 (0.17), residues: 2076 helix: 4.29 (0.10), residues: 1488 sheet: 1.60 (0.49), residues: 132 loop : -2.15 (0.23), residues: 456 *********************** 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 292 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 2.120 Fit side-chains outliers start: 55 outliers final: 27 residues processed: 292 average time/residue: 1.2237 time to fit residues: 400.8306 Evaluate side-chains 256 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 2.8586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** I 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 17496 Z= 0.176 Angle : 0.469 4.980 23904 Z= 0.251 Chirality : 0.039 0.149 2856 Planarity : 0.003 0.039 2856 Dihedral : 3.552 14.656 2280 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 1.52 % 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: 4.34 (0.17), residues: 2076 helix: 4.28 (0.10), residues: 1488 sheet: 1.75 (0.50), residues: 132 loop : -2.21 (0.23), residues: 456 *********************** 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 258 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 2.068 Fit side-chains outliers start: 29 outliers final: 27 residues processed: 258 average time/residue: 1.3826 time to fit residues: 395.9218 Evaluate side-chains 256 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 2.6372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** ** 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: 0.8576 moved from start: 0.2612 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= 0.223 Angle : 0.499 5.295 23904 Z= 0.268 Chirality : 0.040 0.152 2856 Planarity : 0.003 0.039 2856 Dihedral : 3.615 14.735 2280 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 1.47 % 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: 4.20 (0.16), residues: 2076 helix: 4.16 (0.10), residues: 1488 sheet: 1.65 (0.49), residues: 132 loop : -2.17 (0.23), residues: 456 ********************** 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 263 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 235 time to evaluate : 2.183 Fit side-chains outliers start: 28 outliers final: 27 residues processed: 263 average time/residue: 1.3207 time to fit residues: 386.7603 Evaluate side-chains 252 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 2.5860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN ** 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 98 GLN ** L 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075404 restraints weight = 25813.654| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.96 r_work: 0.2819 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2594 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= 0.187 Angle : 0.483 5.113 23904 Z= 0.258 Chirality : 0.039 0.147 2856 Planarity : 0.003 0.039 2856 Dihedral : 3.556 14.787 2280 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 1.62 % 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: 4.29 (0.16), residues: 2076 helix: 4.24 (0.10), residues: 1488 sheet: 1.69 (0.50), residues: 132 loop : -2.20 (0.23), residues: 456 =============================================================================== Job complete usr+sys time: 6034.80 seconds wall clock time: 107 minutes 52.93 seconds (6472.93 seconds total)