Starting phenix.real_space_refine on Sat Mar 23 06:30:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et1_28583/03_2024/8et1_28583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et1_28583/03_2024/8et1_28583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et1_28583/03_2024/8et1_28583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et1_28583/03_2024/8et1_28583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et1_28583/03_2024/8et1_28583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et1_28583/03_2024/8et1_28583.pdb" } resolution = 4.48 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= 0.003 sd= 0.031 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 144 5.16 5 C 22752 2.51 5 N 6432 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "G GLU 15": "OE1" <-> "OE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "I GLU 15": "OE1" <-> "OE2" Residue "J GLU 15": "OE1" <-> "OE2" Residue "K GLU 15": "OE1" <-> "OE2" Residue "L GLU 15": "OE1" <-> "OE2" Residue "M GLU 15": "OE1" <-> "OE2" Residue "N GLU 15": "OE1" <-> "OE2" Residue "O GLU 15": "OE1" <-> "OE2" Residue "P GLU 15": "OE1" <-> "OE2" Residue "Q GLU 15": "OE1" <-> "OE2" Residue "R GLU 15": "OE1" <-> "OE2" Residue "S GLU 15": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "U GLU 15": "OE1" <-> "OE2" Residue "V GLU 15": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "X GLU 15": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35976 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "B" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "C" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "D" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "E" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "F" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "G" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "H" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "I" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "K" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "M" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "N" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "O" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "P" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "Q" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "R" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "S" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "T" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "U" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "V" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "W" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Chain: "X" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Time building chain proxies: 18.30, per 1000 atoms: 0.51 Number of scatterers: 35976 At special positions: 0 Unit cell: (270.58, 270.58, 53.12, 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 144 16.00 O 6648 8.00 N 6432 7.00 C 22752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 12.66 Conformation dependent library (CDL) restraints added in 6.1 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 96 sheets defined 18.1% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'D' and resid 4 through 17 Processing helix chain 'D' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 152 Processing helix chain 'E' and resid 4 through 17 Processing helix chain 'E' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA E 131 " --> pdb=" O GLN E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 152 Processing helix chain 'F' and resid 4 through 17 Processing helix chain 'F' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA F 131 " --> pdb=" O GLN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 152 Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 127 through 136 removed outlier: 3.669A pdb=" N ALA G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 152 Processing helix chain 'H' and resid 4 through 17 Processing helix chain 'H' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA H 131 " --> pdb=" O GLN H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 152 Processing helix chain 'I' and resid 4 through 17 Processing helix chain 'I' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA I 131 " --> pdb=" O GLN I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'J' and resid 4 through 17 Processing helix chain 'J' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA J 131 " --> pdb=" O GLN J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 152 Processing helix chain 'K' and resid 4 through 17 Processing helix chain 'K' and resid 127 through 136 removed outlier: 3.667A pdb=" N ALA K 131 " --> pdb=" O GLN K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'L' and resid 4 through 17 Processing helix chain 'L' and resid 127 through 136 removed outlier: 3.667A pdb=" N ALA L 131 " --> pdb=" O GLN L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 152 Processing helix chain 'M' and resid 4 through 17 Processing helix chain 'M' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 152 Processing helix chain 'N' and resid 4 through 17 Processing helix chain 'N' and resid 127 through 136 removed outlier: 3.669A pdb=" N ALA N 131 " --> pdb=" O GLN N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 152 Processing helix chain 'O' and resid 4 through 17 Processing helix chain 'O' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA O 131 " --> pdb=" O GLN O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 152 Processing helix chain 'P' and resid 4 through 17 Processing helix chain 'P' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA P 131 " --> pdb=" O GLN P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 152 Processing helix chain 'Q' and resid 4 through 17 Processing helix chain 'Q' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA Q 131 " --> pdb=" O GLN Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 152 Processing helix chain 'R' and resid 4 through 17 Processing helix chain 'R' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA R 131 " --> pdb=" O GLN R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 152 Processing helix chain 'S' and resid 4 through 17 Processing helix chain 'S' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA S 131 " --> pdb=" O GLN S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 152 Processing helix chain 'T' and resid 4 through 17 Processing helix chain 'T' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA T 131 " --> pdb=" O GLN T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 152 Processing helix chain 'U' and resid 4 through 17 Processing helix chain 'U' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA U 131 " --> pdb=" O GLN U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 144 through 152 Processing helix chain 'V' and resid 4 through 17 Processing helix chain 'V' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA V 131 " --> pdb=" O GLN V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 144 through 152 Processing helix chain 'W' and resid 4 through 17 Processing helix chain 'W' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA W 131 " --> pdb=" O GLN W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 144 through 152 Processing helix chain 'X' and resid 4 through 17 Processing helix chain 'X' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA X 131 " --> pdb=" O GLN X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 152 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 213 Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'C' and resid 84 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AB4, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'D' and resid 84 through 90 Processing sheet with id=AB7, first strand: chain 'D' and resid 211 through 213 Processing sheet with id=AB8, first strand: chain 'E' and resid 23 through 24 Processing sheet with id=AB9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'E' and resid 84 through 90 Processing sheet with id=AC2, first strand: chain 'E' and resid 211 through 213 Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AC4, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 90 Processing sheet with id=AC6, first strand: chain 'F' and resid 211 through 213 Processing sheet with id=AC7, first strand: chain 'G' and resid 23 through 24 Processing sheet with id=AC8, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'G' and resid 84 through 90 Processing sheet with id=AD1, first strand: chain 'G' and resid 211 through 213 Processing sheet with id=AD2, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=AD3, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'H' and resid 84 through 90 Processing sheet with id=AD5, first strand: chain 'H' and resid 211 through 213 Processing sheet with id=AD6, first strand: chain 'I' and resid 23 through 24 Processing sheet with id=AD7, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AD8, first strand: chain 'I' and resid 84 through 90 Processing sheet with id=AD9, first strand: chain 'I' and resid 211 through 213 Processing sheet with id=AE1, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AE2, first strand: chain 'J' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'J' and resid 84 through 90 Processing sheet with id=AE4, first strand: chain 'J' and resid 211 through 213 Processing sheet with id=AE5, first strand: chain 'K' and resid 23 through 24 Processing sheet with id=AE6, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AE7, first strand: chain 'K' and resid 84 through 90 Processing sheet with id=AE8, first strand: chain 'K' and resid 211 through 213 Processing sheet with id=AE9, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AF1, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=AF2, first strand: chain 'L' and resid 84 through 90 Processing sheet with id=AF3, first strand: chain 'L' and resid 211 through 213 Processing sheet with id=AF4, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=AF5, first strand: chain 'M' and resid 43 through 44 Processing sheet with id=AF6, first strand: chain 'M' and resid 84 through 90 Processing sheet with id=AF7, first strand: chain 'M' and resid 211 through 213 Processing sheet with id=AF8, first strand: chain 'N' and resid 23 through 24 Processing sheet with id=AF9, first strand: chain 'N' and resid 43 through 44 Processing sheet with id=AG1, first strand: chain 'N' and resid 84 through 90 Processing sheet with id=AG2, first strand: chain 'N' and resid 211 through 213 Processing sheet with id=AG3, first strand: chain 'O' and resid 23 through 24 Processing sheet with id=AG4, first strand: chain 'O' and resid 43 through 44 Processing sheet with id=AG5, first strand: chain 'O' and resid 84 through 90 Processing sheet with id=AG6, first strand: chain 'O' and resid 211 through 213 Processing sheet with id=AG7, first strand: chain 'P' and resid 23 through 24 Processing sheet with id=AG8, first strand: chain 'P' and resid 43 through 44 Processing sheet with id=AG9, first strand: chain 'P' and resid 84 through 90 Processing sheet with id=AH1, first strand: chain 'P' and resid 211 through 213 Processing sheet with id=AH2, first strand: chain 'Q' and resid 23 through 24 Processing sheet with id=AH3, first strand: chain 'Q' and resid 43 through 44 Processing sheet with id=AH4, first strand: chain 'Q' and resid 84 through 90 Processing sheet with id=AH5, first strand: chain 'Q' and resid 211 through 213 Processing sheet with id=AH6, first strand: chain 'R' and resid 23 through 24 Processing sheet with id=AH7, first strand: chain 'R' and resid 43 through 44 Processing sheet with id=AH8, first strand: chain 'R' and resid 84 through 90 Processing sheet with id=AH9, first strand: chain 'R' and resid 211 through 213 Processing sheet with id=AI1, first strand: chain 'S' and resid 23 through 24 Processing sheet with id=AI2, first strand: chain 'S' and resid 43 through 44 Processing sheet with id=AI3, first strand: chain 'S' and resid 84 through 90 Processing sheet with id=AI4, first strand: chain 'S' and resid 211 through 213 Processing sheet with id=AI5, first strand: chain 'T' and resid 23 through 24 Processing sheet with id=AI6, first strand: chain 'T' and resid 43 through 44 Processing sheet with id=AI7, first strand: chain 'T' and resid 84 through 90 Processing sheet with id=AI8, first strand: chain 'T' and resid 211 through 213 Processing sheet with id=AI9, first strand: chain 'U' and resid 23 through 24 Processing sheet with id=AJ1, first strand: chain 'U' and resid 43 through 44 Processing sheet with id=AJ2, first strand: chain 'U' and resid 84 through 90 Processing sheet with id=AJ3, first strand: chain 'U' and resid 211 through 213 Processing sheet with id=AJ4, first strand: chain 'V' and resid 23 through 24 Processing sheet with id=AJ5, first strand: chain 'V' and resid 43 through 44 Processing sheet with id=AJ6, first strand: chain 'V' and resid 84 through 90 Processing sheet with id=AJ7, first strand: chain 'V' and resid 211 through 213 Processing sheet with id=AJ8, first strand: chain 'W' and resid 23 through 24 Processing sheet with id=AJ9, first strand: chain 'W' and resid 43 through 44 Processing sheet with id=AK1, first strand: chain 'W' and resid 84 through 90 Processing sheet with id=AK2, first strand: chain 'W' and resid 211 through 213 Processing sheet with id=AK3, first strand: chain 'X' and resid 23 through 24 Processing sheet with id=AK4, first strand: chain 'X' and resid 43 through 44 Processing sheet with id=AK5, first strand: chain 'X' and resid 84 through 90 Processing sheet with id=AK6, first strand: chain 'X' and resid 211 through 213 912 hydrogen bonds defined for protein. 2232 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: 9.86 Time building geometry restraints manager: 13.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11952 1.34 - 1.46: 6129 1.46 - 1.57: 18207 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 36528 Sorted by residual: bond pdb=" SD MET J 16 " pdb=" CE MET J 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.78e+00 bond pdb=" SD MET S 16 " pdb=" CE MET S 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" SD MET Q 16 " pdb=" CE MET Q 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" SD MET C 16 " pdb=" CE MET C 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" SD MET W 16 " pdb=" CE MET W 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.75e+00 ... (remaining 36523 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.16: 817 107.16 - 113.87: 20638 113.87 - 120.58: 12768 120.58 - 127.29: 14545 127.29 - 133.99: 192 Bond angle restraints: 48960 Sorted by residual: angle pdb=" CA MET S 16 " pdb=" CB MET S 16 " pdb=" CG MET S 16 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.93e+00 angle pdb=" CA MET V 16 " pdb=" CB MET V 16 " pdb=" CG MET V 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" CA MET O 16 " pdb=" CB MET O 16 " pdb=" CG MET O 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" CA MET H 16 " pdb=" CB MET H 16 " pdb=" CG MET H 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.85e+00 angle pdb=" CA MET R 16 " pdb=" CB MET R 16 " pdb=" CG MET R 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.85e+00 ... (remaining 48955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 19361 15.49 - 30.97: 2071 30.97 - 46.46: 696 46.46 - 61.95: 96 61.95 - 77.44: 48 Dihedral angle restraints: 22272 sinusoidal: 9600 harmonic: 12672 Sorted by residual: dihedral pdb=" CA MET P 16 " pdb=" C MET P 16 " pdb=" N ASP P 17 " pdb=" CA ASP P 17 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA MET J 16 " pdb=" C MET J 16 " pdb=" N ASP J 17 " pdb=" CA ASP J 17 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA MET W 16 " pdb=" C MET W 16 " pdb=" N ASP W 17 " pdb=" CA ASP W 17 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 22269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3238 0.033 - 0.065: 1525 0.065 - 0.098: 420 0.098 - 0.130: 222 0.130 - 0.163: 91 Chirality restraints: 5496 Sorted by residual: chirality pdb=" CA ASN R 154 " pdb=" N ASN R 154 " pdb=" C ASN R 154 " pdb=" CB ASN R 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ASN J 154 " pdb=" N ASN J 154 " pdb=" C ASN J 154 " pdb=" CB ASN J 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA ASN F 154 " pdb=" N ASN F 154 " pdb=" C ASN F 154 " pdb=" CB ASN F 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 5493 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE U 214 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO U 215 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO U 215 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO U 215 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 214 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO I 215 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO I 215 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 215 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE P 214 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO P 215 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO P 215 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO P 215 " 0.029 5.00e-02 4.00e+02 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2259 2.72 - 3.27: 38320 3.27 - 3.81: 60291 3.81 - 4.36: 68571 4.36 - 4.90: 111979 Nonbonded interactions: 281420 Sorted by model distance: nonbonded pdb=" O GLY F 66 " pdb=" OH TYR F 129 " model vdw 2.180 2.440 nonbonded pdb=" O GLY I 66 " pdb=" OH TYR I 129 " model vdw 2.180 2.440 nonbonded pdb=" O GLY T 66 " pdb=" OH TYR T 129 " model vdw 2.180 2.440 nonbonded pdb=" O GLY O 66 " pdb=" OH TYR O 129 " model vdw 2.180 2.440 nonbonded pdb=" O GLY L 66 " pdb=" OH TYR L 129 " model vdw 2.181 2.440 ... (remaining 281415 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 group one per residue 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: 1.090 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: 0.030 Extract box with map and model: 5.860 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 84.710 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.370 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 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 0.033 36528 Z= 0.210 Angle : 0.818 7.476 48960 Z= 0.471 Chirality : 0.046 0.163 5496 Planarity : 0.005 0.052 6240 Dihedral : 15.011 77.436 13968 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 29.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.12), residues: 4176 helix: 0.33 (0.20), residues: 744 sheet: -1.61 (0.19), residues: 888 loop : -3.73 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP S 69 HIS 0.012 0.003 HIS E 38 PHE 0.015 0.001 PHE J 5 TYR 0.007 0.002 TYR G 156 ARG 0.006 0.001 ARG L 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 4.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.7391 (p) cc_final: 0.7178 (p) REVERT: E 164 THR cc_start: 0.7586 (p) cc_final: 0.7356 (p) REVERT: G 164 THR cc_start: 0.7384 (p) cc_final: 0.7162 (p) REVERT: H 17 ASP cc_start: 0.7390 (p0) cc_final: 0.6713 (p0) REVERT: J 17 ASP cc_start: 0.7146 (p0) cc_final: 0.6540 (p0) REVERT: J 164 THR cc_start: 0.7653 (p) cc_final: 0.7414 (p) REVERT: K 164 THR cc_start: 0.6781 (p) cc_final: 0.6489 (p) REVERT: L 17 ASP cc_start: 0.7215 (p0) cc_final: 0.6969 (p0) REVERT: N 37 PHE cc_start: 0.8555 (m-80) cc_final: 0.8346 (m-80) REVERT: P 164 THR cc_start: 0.6754 (p) cc_final: 0.6508 (p) REVERT: V 164 THR cc_start: 0.7282 (p) cc_final: 0.7070 (p) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.5956 time to fit residues: 295.7657 Evaluate side-chains 195 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 1.9990 chunk 327 optimal weight: 0.4980 chunk 181 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 338 optimal weight: 0.0980 chunk 131 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 ASN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 ASN ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 HIS ** J 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 ASN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 ASN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 ASN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 ASN ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 202 ASN ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 202 ASN ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 HIS ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 202 ASN ** Q 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 HIS ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 HIS ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 202 ASN ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 ASN ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 202 ASN ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 ASN ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 HIS ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 202 ASN ** W 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 HIS ** X 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 202 ASN ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36528 Z= 0.178 Angle : 0.660 8.010 48960 Z= 0.361 Chirality : 0.044 0.156 5496 Planarity : 0.005 0.050 6240 Dihedral : 6.057 20.023 4752 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 0.27 % Allowed : 9.36 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.12), residues: 4176 helix: 0.37 (0.19), residues: 768 sheet: -1.38 (0.18), residues: 840 loop : -3.73 (0.09), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 69 HIS 0.008 0.002 HIS L 38 PHE 0.016 0.001 PHE D 5 TYR 0.014 0.002 TYR C 52 ARG 0.007 0.001 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 293 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8209 (mmp) cc_final: 0.7818 (mmm) REVERT: D 164 THR cc_start: 0.7567 (p) cc_final: 0.7366 (p) REVERT: E 164 THR cc_start: 0.7649 (p) cc_final: 0.7418 (p) REVERT: G 164 THR cc_start: 0.7461 (p) cc_final: 0.7247 (p) REVERT: H 37 PHE cc_start: 0.8434 (m-80) cc_final: 0.8067 (m-80) REVERT: L 17 ASP cc_start: 0.8354 (p0) cc_final: 0.8043 (p0) REVERT: M 22 MET cc_start: 0.8788 (mmp) cc_final: 0.8396 (mmm) REVERT: P 164 THR cc_start: 0.6969 (p) cc_final: 0.6758 (p) REVERT: Q 164 THR cc_start: 0.6987 (p) cc_final: 0.6755 (p) REVERT: R 22 MET cc_start: 0.8372 (mmp) cc_final: 0.8142 (mmm) REVERT: V 164 THR cc_start: 0.7415 (p) cc_final: 0.7205 (p) outliers start: 11 outliers final: 7 residues processed: 304 average time/residue: 0.5036 time to fit residues: 242.8890 Evaluate side-chains 185 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 393 optimal weight: 0.9980 chunk 424 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 389 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 315 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS B 128 GLN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 GLN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 GLN ** J 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 GLN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 GLN ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 GLN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 GLN ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 GLN ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 GLN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 GLN ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 128 GLN ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 128 GLN ** X 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36528 Z= 0.258 Angle : 0.732 9.825 48960 Z= 0.398 Chirality : 0.046 0.194 5496 Planarity : 0.006 0.050 6240 Dihedral : 6.724 21.136 4752 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 33.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 0.50 % Allowed : 5.81 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.11), residues: 4176 helix: -0.29 (0.18), residues: 768 sheet: 0.07 (0.22), residues: 552 loop : -4.00 (0.09), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 69 HIS 0.009 0.002 HIS L 38 PHE 0.021 0.002 PHE W 5 TYR 0.014 0.002 TYR G 52 ARG 0.010 0.001 ARG U 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 5.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8763 (mmp) cc_final: 0.8552 (mmm) REVERT: A 128 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7565 (pp30) REVERT: B 128 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7256 (pp30) REVERT: H 22 MET cc_start: 0.8434 (mmp) cc_final: 0.8197 (mmm) REVERT: I 128 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7330 (pp30) REVERT: J 22 MET cc_start: 0.8654 (mmp) cc_final: 0.8383 (mmm) REVERT: J 37 PHE cc_start: 0.8700 (m-80) cc_final: 0.8496 (m-80) REVERT: J 128 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7327 (pp30) REVERT: L 17 ASP cc_start: 0.8577 (p0) cc_final: 0.7843 (p0) REVERT: N 59 MET cc_start: 0.7935 (mpp) cc_final: 0.7633 (mpp) REVERT: N 128 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7278 (pp30) REVERT: Q 164 THR cc_start: 0.7363 (p) cc_final: 0.7139 (p) REVERT: R 22 MET cc_start: 0.8783 (mmp) cc_final: 0.8496 (mmm) REVERT: S 22 MET cc_start: 0.8913 (mmp) cc_final: 0.8548 (mmm) REVERT: S 128 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7279 (pp30) REVERT: T 128 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7425 (pp30) outliers start: 20 outliers final: 0 residues processed: 260 average time/residue: 0.5422 time to fit residues: 222.1470 Evaluate side-chains 182 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 263 optimal weight: 0.7980 chunk 394 optimal weight: 5.9990 chunk 417 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS H 128 GLN H 154 ASN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 154 ASN ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 154 ASN ** Q 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 GLN R 154 ASN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 154 ASN ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 128 GLN ** X 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36528 Z= 0.269 Angle : 0.759 10.618 48960 Z= 0.414 Chirality : 0.047 0.208 5496 Planarity : 0.007 0.053 6240 Dihedral : 6.902 21.798 4752 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 36.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 0.32 % Allowed : 4.59 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.11), residues: 4176 helix: -0.48 (0.18), residues: 768 sheet: -0.35 (0.21), residues: 552 loop : -4.09 (0.08), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 69 HIS 0.009 0.002 HIS H 51 PHE 0.025 0.002 PHE B 5 TYR 0.010 0.002 TYR C 52 ARG 0.010 0.001 ARG H 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 251 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8624 (mmp) cc_final: 0.8391 (mmm) REVERT: C 128 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7201 (pp30) REVERT: D 22 MET cc_start: 0.8651 (mmp) cc_final: 0.8413 (mmm) REVERT: F 22 MET cc_start: 0.8714 (mmp) cc_final: 0.8385 (mmm) REVERT: F 219 THR cc_start: 0.6960 (p) cc_final: 0.6666 (t) REVERT: H 128 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7224 (pp30) REVERT: L 128 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7261 (mt0) REVERT: O 37 PHE cc_start: 0.8499 (m-80) cc_final: 0.8175 (m-80) REVERT: R 22 MET cc_start: 0.8993 (mmp) cc_final: 0.8606 (mmm) REVERT: T 219 THR cc_start: 0.6629 (p) cc_final: 0.6195 (t) REVERT: U 219 THR cc_start: 0.6002 (p) cc_final: 0.5792 (t) REVERT: V 219 THR cc_start: 0.6029 (p) cc_final: 0.5648 (t) REVERT: X 22 MET cc_start: 0.8764 (mmp) cc_final: 0.8435 (mmm) REVERT: X 219 THR cc_start: 0.6818 (p) cc_final: 0.6568 (t) outliers start: 13 outliers final: 0 residues processed: 264 average time/residue: 0.5280 time to fit residues: 220.5378 Evaluate side-chains 172 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 6 optimal weight: 0.1980 chunk 310 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 356 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 154 ASN ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 211 GLN F 128 GLN F 154 ASN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 ASN ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 GLN I 51 HIS I 154 ASN ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 ASN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 HIS ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 ASN ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 GLN ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 GLN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 ASN ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 HIS ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 51 HIS ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 ASN W 211 GLN X 128 GLN X 154 ASN ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36528 Z= 0.201 Angle : 0.707 9.608 48960 Z= 0.382 Chirality : 0.046 0.179 5496 Planarity : 0.006 0.056 6240 Dihedral : 6.533 21.648 4752 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 30.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.45 % Allowed : 5.51 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.11), residues: 4176 helix: -0.13 (0.19), residues: 768 sheet: -1.29 (0.17), residues: 792 loop : -3.90 (0.09), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 69 HIS 0.010 0.002 HIS T 51 PHE 0.015 0.001 PHE C 5 TYR 0.006 0.001 TYR A 207 ARG 0.008 0.001 ARG O 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 267 time to evaluate : 4.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 THR cc_start: 0.6988 (p) cc_final: 0.6508 (t) REVERT: D 220 MET cc_start: 0.0577 (mmm) cc_final: 0.0339 (mmt) REVERT: F 164 THR cc_start: 0.7489 (p) cc_final: 0.7203 (p) REVERT: F 219 THR cc_start: 0.6885 (p) cc_final: 0.6593 (t) REVERT: G 85 GLN cc_start: 0.8074 (pp30) cc_final: 0.7817 (pp30) REVERT: J 164 THR cc_start: 0.7351 (p) cc_final: 0.7116 (p) REVERT: L 22 MET cc_start: 0.8464 (mmp) cc_final: 0.8245 (mmm) REVERT: N 22 MET cc_start: 0.8296 (mmp) cc_final: 0.8015 (mmm) REVERT: O 37 PHE cc_start: 0.8437 (m-80) cc_final: 0.8127 (m-80) REVERT: P 164 THR cc_start: 0.7325 (p) cc_final: 0.7085 (p) REVERT: P 220 MET cc_start: 0.0288 (mmm) cc_final: 0.0004 (mmt) REVERT: R 22 MET cc_start: 0.8927 (mmp) cc_final: 0.8661 (mmm) REVERT: R 219 THR cc_start: 0.6964 (p) cc_final: 0.6567 (t) REVERT: T 219 THR cc_start: 0.6528 (p) cc_final: 0.6083 (t) REVERT: U 37 PHE cc_start: 0.8438 (m-80) cc_final: 0.8160 (m-80) REVERT: U 219 THR cc_start: 0.6021 (p) cc_final: 0.5682 (t) REVERT: V 219 THR cc_start: 0.5972 (p) cc_final: 0.5554 (t) REVERT: X 219 THR cc_start: 0.6904 (p) cc_final: 0.6488 (t) outliers start: 18 outliers final: 0 residues processed: 285 average time/residue: 0.5039 time to fit residues: 228.7670 Evaluate side-chains 179 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 10.0000 chunk 376 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 417 optimal weight: 3.9990 chunk 346 optimal weight: 0.6980 chunk 193 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 GLN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 GLN ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 211 GLN R 128 GLN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN U 154 ASN ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 128 GLN ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 128 GLN ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36528 Z= 0.206 Angle : 0.704 8.719 48960 Z= 0.383 Chirality : 0.046 0.174 5496 Planarity : 0.006 0.060 6240 Dihedral : 6.482 21.003 4752 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 30.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 0.25 % Allowed : 3.62 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.11), residues: 4176 helix: -0.08 (0.19), residues: 768 sheet: -1.29 (0.17), residues: 792 loop : -3.88 (0.09), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 69 HIS 0.008 0.002 HIS L 38 PHE 0.016 0.001 PHE D 5 TYR 0.011 0.002 TYR R 52 ARG 0.007 0.001 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 270 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 MET cc_start: 0.8203 (mmp) cc_final: 0.7874 (mmm) REVERT: B 219 THR cc_start: 0.6956 (p) cc_final: 0.6465 (t) REVERT: D 220 MET cc_start: 0.0594 (mmm) cc_final: 0.0367 (mmt) REVERT: F 164 THR cc_start: 0.7433 (p) cc_final: 0.7141 (p) REVERT: G 85 GLN cc_start: 0.8264 (pp30) cc_final: 0.8038 (pp30) REVERT: J 164 THR cc_start: 0.7326 (p) cc_final: 0.7090 (p) REVERT: L 22 MET cc_start: 0.8578 (mmp) cc_final: 0.8303 (mmm) REVERT: M 85 GLN cc_start: 0.8139 (pp30) cc_final: 0.7913 (pp30) REVERT: O 37 PHE cc_start: 0.8398 (m-80) cc_final: 0.8184 (m-80) REVERT: O 128 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.7117 (pp30) REVERT: P 164 THR cc_start: 0.7222 (p) cc_final: 0.6992 (p) REVERT: P 220 MET cc_start: 0.0270 (mmm) cc_final: 0.0041 (mmt) REVERT: R 22 MET cc_start: 0.8916 (mmp) cc_final: 0.8613 (mmm) REVERT: R 219 THR cc_start: 0.6678 (p) cc_final: 0.6302 (t) REVERT: T 219 THR cc_start: 0.6553 (p) cc_final: 0.6083 (t) REVERT: U 37 PHE cc_start: 0.8347 (m-80) cc_final: 0.8089 (m-80) REVERT: U 128 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7393 (pp30) REVERT: U 219 THR cc_start: 0.5838 (p) cc_final: 0.5616 (t) REVERT: V 128 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7690 (pp30) REVERT: X 128 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6898 (pp30) REVERT: X 219 THR cc_start: 0.6904 (p) cc_final: 0.6475 (t) outliers start: 10 outliers final: 1 residues processed: 280 average time/residue: 0.5091 time to fit residues: 225.0288 Evaluate side-chains 184 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 238 optimal weight: 8.9990 chunk 305 optimal weight: 0.0370 chunk 236 optimal weight: 9.9990 chunk 351 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 416 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 overall best weight: 2.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 GLN ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 128 GLN ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36528 Z= 0.217 Angle : 0.709 8.591 48960 Z= 0.387 Chirality : 0.047 0.197 5496 Planarity : 0.006 0.058 6240 Dihedral : 6.583 21.100 4752 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 31.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 0.12 % Allowed : 2.40 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.11), residues: 4176 helix: -0.24 (0.19), residues: 768 sheet: -1.22 (0.18), residues: 792 loop : -3.86 (0.09), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 69 HIS 0.007 0.002 HIS B 38 PHE 0.018 0.001 PHE A 5 TYR 0.012 0.002 TYR L 52 ARG 0.009 0.001 ARG N 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 219 THR cc_start: 0.6436 (p) cc_final: 0.5965 (t) REVERT: D 220 MET cc_start: 0.0625 (mmm) cc_final: 0.0415 (mmt) REVERT: F 164 THR cc_start: 0.7465 (p) cc_final: 0.7171 (p) REVERT: G 85 GLN cc_start: 0.8246 (pp30) cc_final: 0.8045 (pp30) REVERT: G 128 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7541 (pp30) REVERT: J 164 THR cc_start: 0.7359 (p) cc_final: 0.7126 (p) REVERT: K 37 PHE cc_start: 0.8759 (m-80) cc_final: 0.8319 (m-80) REVERT: M 85 GLN cc_start: 0.8259 (pp30) cc_final: 0.8019 (pp30) REVERT: P 164 THR cc_start: 0.7286 (p) cc_final: 0.7039 (p) REVERT: P 220 MET cc_start: 0.0302 (mmm) cc_final: 0.0059 (mmt) REVERT: Q 37 PHE cc_start: 0.8853 (m-80) cc_final: 0.8646 (m-80) REVERT: Q 128 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7057 (pp30) REVERT: R 219 THR cc_start: 0.6826 (p) cc_final: 0.6473 (t) REVERT: T 219 THR cc_start: 0.6589 (p) cc_final: 0.6100 (t) REVERT: U 219 THR cc_start: 0.5811 (p) cc_final: 0.5598 (t) REVERT: W 128 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7126 (pp30) REVERT: X 219 THR cc_start: 0.6658 (p) cc_final: 0.6278 (t) outliers start: 5 outliers final: 2 residues processed: 279 average time/residue: 0.5152 time to fit residues: 227.4087 Evaluate side-chains 179 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 0.8980 chunk 166 optimal weight: 0.1980 chunk 248 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 283 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 GLN ** J 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 36528 Z= 0.160 Angle : 0.657 9.109 48960 Z= 0.359 Chirality : 0.046 0.192 5496 Planarity : 0.006 0.058 6240 Dihedral : 6.187 20.236 4752 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.12), residues: 4176 helix: 0.07 (0.20), residues: 768 sheet: -0.97 (0.18), residues: 792 loop : -3.76 (0.09), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP M 69 HIS 0.008 0.002 HIS R 38 PHE 0.010 0.001 PHE B 5 TYR 0.010 0.001 TYR N 52 ARG 0.007 0.001 ARG N 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 220 MET cc_start: 0.0572 (mmm) cc_final: 0.0347 (mmt) REVERT: F 164 THR cc_start: 0.7274 (p) cc_final: 0.6974 (p) REVERT: J 21 ASP cc_start: 0.8969 (t0) cc_final: 0.8348 (p0) REVERT: J 164 THR cc_start: 0.7453 (p) cc_final: 0.7216 (p) REVERT: M 164 THR cc_start: 0.7158 (p) cc_final: 0.6927 (p) REVERT: O 37 PHE cc_start: 0.8234 (m-80) cc_final: 0.7941 (m-80) REVERT: P 164 THR cc_start: 0.7062 (p) cc_final: 0.6810 (p) REVERT: P 220 MET cc_start: 0.0214 (mmm) cc_final: -0.0026 (mmt) REVERT: Q 37 PHE cc_start: 0.8689 (m-80) cc_final: 0.8453 (m-80) REVERT: R 219 THR cc_start: 0.6870 (p) cc_final: 0.6472 (t) REVERT: S 164 THR cc_start: 0.7219 (p) cc_final: 0.6978 (p) REVERT: T 219 THR cc_start: 0.6466 (p) cc_final: 0.5971 (t) REVERT: U 219 THR cc_start: 0.5647 (p) cc_final: 0.5438 (t) REVERT: V 164 THR cc_start: 0.7188 (p) cc_final: 0.6961 (p) REVERT: V 220 MET cc_start: 0.0167 (mmm) cc_final: -0.0147 (mmt) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.5102 time to fit residues: 253.2473 Evaluate side-chains 182 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 10.0000 chunk 398 optimal weight: 0.1980 chunk 363 optimal weight: 0.0470 chunk 388 optimal weight: 4.9990 chunk 233 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 304 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 chunk 366 optimal weight: 0.7980 chunk 386 optimal weight: 9.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 ASN ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 ASN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 36528 Z= 0.166 Angle : 0.667 10.025 48960 Z= 0.364 Chirality : 0.045 0.197 5496 Planarity : 0.006 0.073 6240 Dihedral : 6.052 20.867 4752 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.02 % Allowed : 1.02 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.12), residues: 4176 helix: 0.12 (0.20), residues: 768 sheet: -1.13 (0.17), residues: 840 loop : -3.73 (0.09), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 69 HIS 0.007 0.001 HIS M 38 PHE 0.017 0.001 PHE B 5 TYR 0.009 0.001 TYR R 52 ARG 0.010 0.001 ARG O 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.7436 (p) cc_final: 0.7231 (p) REVERT: C 22 MET cc_start: 0.8635 (mpp) cc_final: 0.8285 (pmm) REVERT: D 164 THR cc_start: 0.7171 (p) cc_final: 0.6945 (p) REVERT: E 22 MET cc_start: 0.8153 (mmt) cc_final: 0.7533 (mmm) REVERT: K 22 MET cc_start: 0.8114 (mmt) cc_final: 0.7292 (mmm) REVERT: K 164 THR cc_start: 0.7362 (p) cc_final: 0.7118 (p) REVERT: M 164 THR cc_start: 0.7222 (p) cc_final: 0.6971 (p) REVERT: O 37 PHE cc_start: 0.8390 (m-80) cc_final: 0.8066 (m-80) REVERT: P 164 THR cc_start: 0.7113 (p) cc_final: 0.6894 (p) REVERT: Q 37 PHE cc_start: 0.8584 (m-80) cc_final: 0.8382 (m-80) REVERT: S 164 THR cc_start: 0.7276 (p) cc_final: 0.7041 (p) REVERT: T 37 PHE cc_start: 0.8260 (m-80) cc_final: 0.8056 (m-80) REVERT: T 219 THR cc_start: 0.6894 (p) cc_final: 0.6421 (t) REVERT: U 219 THR cc_start: 0.5646 (p) cc_final: 0.5433 (t) REVERT: V 21 ASP cc_start: 0.8408 (t70) cc_final: 0.8038 (p0) REVERT: V 164 THR cc_start: 0.7215 (p) cc_final: 0.6978 (p) REVERT: X 21 ASP cc_start: 0.8815 (t0) cc_final: 0.8585 (p0) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.5059 time to fit residues: 242.6957 Evaluate side-chains 178 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 8.9990 chunk 410 optimal weight: 0.5980 chunk 250 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 285 optimal weight: 5.9990 chunk 430 optimal weight: 4.9990 chunk 396 optimal weight: 7.9990 chunk 342 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 ASN ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36528 Z= 0.167 Angle : 0.667 10.877 48960 Z= 0.363 Chirality : 0.045 0.219 5496 Planarity : 0.006 0.086 6240 Dihedral : 5.987 20.518 4752 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.02 % Allowed : 0.45 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.12), residues: 4176 helix: 0.19 (0.20), residues: 768 sheet: -1.08 (0.17), residues: 840 loop : -3.69 (0.09), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 69 HIS 0.009 0.001 HIS G 38 PHE 0.011 0.001 PHE V 5 TYR 0.014 0.001 TYR L 52 ARG 0.010 0.001 ARG U 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 4.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 164 THR cc_start: 0.7117 (p) cc_final: 0.6888 (p) REVERT: E 22 MET cc_start: 0.8393 (mmt) cc_final: 0.7591 (mmm) REVERT: K 22 MET cc_start: 0.8338 (mmt) cc_final: 0.7485 (mmm) REVERT: K 164 THR cc_start: 0.7263 (p) cc_final: 0.7020 (p) REVERT: M 164 THR cc_start: 0.7101 (p) cc_final: 0.6862 (p) REVERT: O 37 PHE cc_start: 0.8333 (m-80) cc_final: 0.8020 (m-80) REVERT: P 164 THR cc_start: 0.7051 (p) cc_final: 0.6827 (p) REVERT: S 164 THR cc_start: 0.7185 (p) cc_final: 0.6939 (p) REVERT: T 219 THR cc_start: 0.6866 (p) cc_final: 0.6385 (t) REVERT: V 164 THR cc_start: 0.7182 (p) cc_final: 0.6964 (p) REVERT: W 37 PHE cc_start: 0.8583 (m-80) cc_final: 0.8370 (m-80) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.5129 time to fit residues: 234.7544 Evaluate side-chains 178 residues out of total 4008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 4.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 0.2980 chunk 365 optimal weight: 0.0980 chunk 104 optimal weight: 6.9990 chunk 316 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 343 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.089745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.079598 restraints weight = 266023.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.080928 restraints weight = 205640.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.081955 restraints weight = 165088.941| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36528 Z= 0.243 Angle : 0.737 10.319 48960 Z= 0.402 Chirality : 0.047 0.173 5496 Planarity : 0.007 0.082 6240 Dihedral : 6.450 21.850 4752 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 32.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 0.02 % Allowed : 0.72 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.11), residues: 4176 helix: 0.04 (0.20), residues: 720 sheet: -1.13 (0.17), residues: 840 loop : -3.73 (0.09), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 69 HIS 0.020 0.002 HIS H 38 PHE 0.019 0.002 PHE O 5 TYR 0.012 0.002 TYR V 207 ARG 0.013 0.001 ARG U 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5857.93 seconds wall clock time: 109 minutes 12.75 seconds (6552.75 seconds total)