Starting phenix.real_space_refine on Sun Mar 17 15:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/03_2024/7tgg_25881.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/03_2024/7tgg_25881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/03_2024/7tgg_25881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/03_2024/7tgg_25881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/03_2024/7tgg_25881.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/03_2024/7tgg_25881.pdb" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.023 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 15 5.16 5 C 11445 2.51 5 N 2985 2.21 5 O 3810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 71": "OD1" <-> "OD2" Residue "C PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "E PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "G PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "I PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "K PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 71": "OD1" <-> "OD2" Residue "M PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 71": "OD1" <-> "OD2" Residue "O PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "Q PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 71": "OD1" <-> "OD2" Residue "S PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 71": "OD1" <-> "OD2" Residue "U PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 71": "OD1" <-> "OD2" Residue "W PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 71": "OD1" <-> "OD2" Residue "Y PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 71": "OD1" <-> "OD2" Residue "0 ASP 71": "OD1" <-> "OD2" Residue "2 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 71": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18255 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "a" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "B" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "E" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "F" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "G" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "I" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "J" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "K" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "L" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "M" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "N" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "O" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "P" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "Q" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "R" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "S" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "T" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "U" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "V" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "W" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "X" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "Y" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "Z" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "0" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "1" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "2" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Time building chain proxies: 9.84, per 1000 atoms: 0.54 Number of scatterers: 18255 At special positions: 0 Unit cell: (83.16, 83.16, 246.24, 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 15 16.00 O 3810 8.00 N 2985 7.00 C 11445 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: 7.25 Conformation dependent library (CDL) restraints added in 3.5 seconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4530 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 27.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA B 31 " --> pdb=" O TYR B 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA F 31 " --> pdb=" O TYR F 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL H 10 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA H 31 " --> pdb=" O TYR H 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR H 45 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL J 10 " --> pdb=" O LEU J 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA J 11 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE J 15 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR J 45 " --> pdb=" O ARG J 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL L 10 " --> pdb=" O LEU L 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA L 31 " --> pdb=" O TYR L 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR L 45 " --> pdb=" O ARG L 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL N 10 " --> pdb=" O LEU N 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA N 31 " --> pdb=" O TYR N 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL P 10 " --> pdb=" O LEU P 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA P 31 " --> pdb=" O TYR P 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR P 45 " --> pdb=" O ARG P 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL R 10 " --> pdb=" O LEU R 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA R 11 " --> pdb=" O LEU R 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA R 31 " --> pdb=" O TYR R 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR R 45 " --> pdb=" O ARG R 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL T 10 " --> pdb=" O LEU T 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA T 31 " --> pdb=" O TYR T 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL V 10 " --> pdb=" O LEU V 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA V 11 " --> pdb=" O LEU V 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE V 15 " --> pdb=" O ALA V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA V 31 " --> pdb=" O TYR V 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR V 45 " --> pdb=" O ARG V 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA X 11 " --> pdb=" O LEU X 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE X 15 " --> pdb=" O ALA X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA X 31 " --> pdb=" O TYR X 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR X 45 " --> pdb=" O ARG X 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL Z 10 " --> pdb=" O LEU Z 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 11 " --> pdb=" O LEU Z 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE Z 15 " --> pdb=" O ALA Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA Z 31 " --> pdb=" O TYR Z 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR Z 45 " --> pdb=" O ARG Z 41 " (cutoff:3.500A) Processing helix chain '1' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL 1 10 " --> pdb=" O LEU 1 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA 1 11 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE 1 15 " --> pdb=" O ALA 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA 1 31 " --> pdb=" O TYR 1 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR 1 45 " --> pdb=" O ARG 1 41 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'a' and resid 22 through 28 Processing sheet with id= 2, first strand: chain 'C' and resid 22 through 28 Processing sheet with id= 3, first strand: chain 'E' and resid 22 through 28 Processing sheet with id= 4, first strand: chain 'G' and resid 22 through 28 Processing sheet with id= 5, first strand: chain 'I' and resid 22 through 28 Processing sheet with id= 6, first strand: chain 'K' and resid 22 through 28 Processing sheet with id= 7, first strand: chain 'M' and resid 22 through 28 Processing sheet with id= 8, first strand: chain 'O' and resid 22 through 28 Processing sheet with id= 9, first strand: chain 'Q' and resid 22 through 28 Processing sheet with id= 10, first strand: chain 'S' and resid 22 through 28 Processing sheet with id= 11, first strand: chain 'U' and resid 22 through 28 Processing sheet with id= 12, first strand: chain 'W' and resid 22 through 28 Processing sheet with id= 13, first strand: chain 'Y' and resid 22 through 28 Processing sheet with id= 14, first strand: chain '0' and resid 22 through 28 Processing sheet with id= 15, first strand: chain '2' and resid 22 through 28 660 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5880 1.34 - 1.46: 3412 1.46 - 1.57: 9263 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 18585 Sorted by residual: bond pdb=" CA THR K 15 " pdb=" CB THR K 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 2.00e+00 bond pdb=" CA THR W 15 " pdb=" CB THR W 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 1.96e+00 bond pdb=" CA THR 2 15 " pdb=" CB THR 2 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 1.94e+00 bond pdb=" CA THR O 15 " pdb=" CB THR O 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 1.93e+00 bond pdb=" CA THR 0 15 " pdb=" CB THR 0 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 1.91e+00 ... (remaining 18580 not shown) Histogram of bond angle deviations from ideal: 101.10 - 107.69: 528 107.69 - 114.27: 10947 114.27 - 120.86: 7359 120.86 - 127.44: 6381 127.44 - 134.03: 120 Bond angle restraints: 25335 Sorted by residual: angle pdb=" CA ASP Q 71 " pdb=" CB ASP Q 71 " pdb=" CG ASP Q 71 " ideal model delta sigma weight residual 112.60 115.10 -2.50 1.00e+00 1.00e+00 6.26e+00 angle pdb=" CA ASP I 71 " pdb=" CB ASP I 71 " pdb=" CG ASP I 71 " ideal model delta sigma weight residual 112.60 115.10 -2.50 1.00e+00 1.00e+00 6.23e+00 angle pdb=" CA ASP O 71 " pdb=" CB ASP O 71 " pdb=" CG ASP O 71 " ideal model delta sigma weight residual 112.60 115.09 -2.49 1.00e+00 1.00e+00 6.19e+00 angle pdb=" CA ASP a 71 " pdb=" CB ASP a 71 " pdb=" CG ASP a 71 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.11e+00 angle pdb=" CA ASP C 71 " pdb=" CB ASP C 71 " pdb=" CG ASP C 71 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.08e+00 ... (remaining 25330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 10125 15.36 - 30.72: 585 30.72 - 46.09: 135 46.09 - 61.45: 45 61.45 - 76.81: 15 Dihedral angle restraints: 10905 sinusoidal: 3870 harmonic: 7035 Sorted by residual: dihedral pdb=" CA PHE I 14 " pdb=" C PHE I 14 " pdb=" N THR I 15 " pdb=" CA THR I 15 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE C 14 " pdb=" C PHE C 14 " pdb=" N THR C 15 " pdb=" CA THR C 15 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE Y 14 " pdb=" C PHE Y 14 " pdb=" N THR Y 15 " pdb=" CA THR Y 15 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 10902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2028 0.038 - 0.077: 800 0.077 - 0.115: 127 0.115 - 0.154: 15 0.154 - 0.192: 45 Chirality restraints: 3015 Sorted by residual: chirality pdb=" CB ILE X 19 " pdb=" CA ILE X 19 " pdb=" CG1 ILE X 19 " pdb=" CG2 ILE X 19 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CB ILE R 19 " pdb=" CA ILE R 19 " pdb=" CG1 ILE R 19 " pdb=" CG2 ILE R 19 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CB ILE J 19 " pdb=" CA ILE J 19 " pdb=" CG1 ILE J 19 " pdb=" CG2 ILE J 19 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 3012 not shown) Planarity restraints: 3225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 73 " -0.016 2.00e-02 2.50e+03 1.24e-02 3.83e+00 pdb=" CG TRP Q 73 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 73 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 73 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 73 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 73 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 73 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 73 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 73 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 73 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 73 " 0.016 2.00e-02 2.50e+03 1.24e-02 3.82e+00 pdb=" CG TRP G 73 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP G 73 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP G 73 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 73 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 73 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 73 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 73 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 73 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 73 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 73 " 0.016 2.00e-02 2.50e+03 1.23e-02 3.81e+00 pdb=" CG TRP M 73 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP M 73 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP M 73 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP M 73 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 73 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 73 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 73 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 73 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP M 73 " 0.005 2.00e-02 2.50e+03 ... (remaining 3222 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 272 2.64 - 3.20: 19501 3.20 - 3.77: 28412 3.77 - 4.33: 39128 4.33 - 4.90: 62500 Nonbonded interactions: 149813 Sorted by model distance: nonbonded pdb=" OG1 THR O 15 " pdb=" NE2 GLN T 23 " model vdw 2.070 2.520 nonbonded pdb=" OG1 THR G 15 " pdb=" NE2 GLN L 23 " model vdw 2.070 2.520 nonbonded pdb=" OG1 THR K 15 " pdb=" NE2 GLN N 23 " model vdw 2.070 2.520 nonbonded pdb=" OG1 THR U 15 " pdb=" NE2 GLN Z 23 " model vdw 2.070 2.520 nonbonded pdb=" OG1 THR C 15 " pdb=" NE2 GLN H 23 " model vdw 2.070 2.520 ... (remaining 149808 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 '0' selection = chain '2' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain '1' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.560 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 47.070 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.004 0.030 18585 Z= 0.235 Angle : 0.714 6.733 25335 Z= 0.413 Chirality : 0.045 0.192 3015 Planarity : 0.007 0.060 3225 Dihedral : 11.742 76.809 6375 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.21 (0.16), residues: 2385 helix: -0.87 (0.19), residues: 675 sheet: 0.48 (0.20), residues: 285 loop : -2.31 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP Q 73 PHE 0.029 0.004 PHE H 24 TYR 0.011 0.002 TYR P 27 ARG 0.005 0.001 ARG V 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8911 (tt) cc_final: 0.8202 (tt) REVERT: a 13 ASP cc_start: 0.8724 (m-30) cc_final: 0.8478 (t0) REVERT: a 101 TRP cc_start: 0.8632 (p-90) cc_final: 0.7701 (p-90) REVERT: C 101 TRP cc_start: 0.8368 (p-90) cc_final: 0.7501 (p-90) REVERT: D 3 LEU cc_start: 0.8893 (tt) cc_final: 0.8322 (tt) REVERT: E 13 ASP cc_start: 0.8660 (m-30) cc_final: 0.8456 (t0) REVERT: E 43 TYR cc_start: 0.9024 (p90) cc_final: 0.8704 (p90) REVERT: E 101 TRP cc_start: 0.8468 (p-90) cc_final: 0.7469 (p-90) REVERT: F 3 LEU cc_start: 0.8952 (tt) cc_final: 0.8243 (tp) REVERT: G 13 ASP cc_start: 0.8637 (m-30) cc_final: 0.8429 (t0) REVERT: G 101 TRP cc_start: 0.8547 (p-90) cc_final: 0.7353 (p-90) REVERT: H 3 LEU cc_start: 0.8951 (tt) cc_final: 0.8427 (tp) REVERT: I 43 TYR cc_start: 0.9062 (p90) cc_final: 0.8785 (p90) REVERT: I 101 TRP cc_start: 0.8416 (p-90) cc_final: 0.8206 (p-90) REVERT: K 13 ASP cc_start: 0.8723 (m-30) cc_final: 0.8516 (t0) REVERT: K 40 ASN cc_start: 0.6570 (m-40) cc_final: 0.5786 (m-40) REVERT: K 42 ASP cc_start: 0.8119 (m-30) cc_final: 0.7829 (t70) REVERT: K 101 TRP cc_start: 0.8476 (p-90) cc_final: 0.7831 (p-90) REVERT: L 3 LEU cc_start: 0.8908 (tt) cc_final: 0.8678 (tt) REVERT: M 101 TRP cc_start: 0.8383 (p-90) cc_final: 0.7434 (p-90) REVERT: N 3 LEU cc_start: 0.8901 (tt) cc_final: 0.8118 (tt) REVERT: P 3 LEU cc_start: 0.8863 (tt) cc_final: 0.8203 (tt) REVERT: Q 13 ASP cc_start: 0.8585 (m-30) cc_final: 0.8330 (t0) REVERT: Q 101 TRP cc_start: 0.8452 (p-90) cc_final: 0.8038 (p90) REVERT: R 3 LEU cc_start: 0.8887 (tt) cc_final: 0.8343 (tt) REVERT: R 5 GLU cc_start: 0.8757 (tt0) cc_final: 0.8491 (tp30) REVERT: S 101 TRP cc_start: 0.8474 (p-90) cc_final: 0.7631 (p-90) REVERT: T 3 LEU cc_start: 0.8803 (tt) cc_final: 0.8012 (tt) REVERT: T 5 GLU cc_start: 0.8888 (tt0) cc_final: 0.8677 (tp30) REVERT: U 13 ASP cc_start: 0.8684 (m-30) cc_final: 0.8347 (t0) REVERT: U 43 TYR cc_start: 0.9084 (p90) cc_final: 0.8577 (p90) REVERT: U 101 TRP cc_start: 0.8525 (p-90) cc_final: 0.7597 (p-90) REVERT: V 3 LEU cc_start: 0.8859 (tt) cc_final: 0.8230 (tt) REVERT: W 101 TRP cc_start: 0.8525 (p-90) cc_final: 0.7549 (p-90) REVERT: X 3 LEU cc_start: 0.8798 (tt) cc_final: 0.7867 (tp) REVERT: Y 40 ASN cc_start: 0.6363 (m-40) cc_final: 0.5660 (m-40) REVERT: Y 101 TRP cc_start: 0.8481 (p-90) cc_final: 0.8054 (p-90) REVERT: Z 3 LEU cc_start: 0.8788 (tt) cc_final: 0.8523 (tp) REVERT: 0 101 TRP cc_start: 0.8560 (p-90) cc_final: 0.8092 (p-90) REVERT: 1 3 LEU cc_start: 0.8835 (tt) cc_final: 0.8336 (tp) REVERT: 1 5 GLU cc_start: 0.8701 (tt0) cc_final: 0.8332 (tp30) REVERT: 2 101 TRP cc_start: 0.8492 (p-90) cc_final: 0.7615 (p-90) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2718 time to fit residues: 154.0654 Evaluate side-chains 222 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN Y 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18585 Z= 0.239 Angle : 0.597 6.579 25335 Z= 0.329 Chirality : 0.043 0.190 3015 Planarity : 0.004 0.040 3225 Dihedral : 7.762 79.521 2565 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2385 helix: 0.79 (0.22), residues: 675 sheet: -0.40 (0.23), residues: 375 loop : -1.78 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 73 PHE 0.018 0.002 PHE H 24 TYR 0.012 0.002 TYR K 43 ARG 0.005 0.001 ARG X 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.096 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: a 43 TYR cc_start: 0.9237 (p90) cc_final: 0.8983 (p90) REVERT: a 101 TRP cc_start: 0.8668 (p-90) cc_final: 0.7697 (p-90) REVERT: C 101 TRP cc_start: 0.8515 (p-90) cc_final: 0.7529 (p-90) REVERT: E 101 TRP cc_start: 0.8590 (p-90) cc_final: 0.7589 (p-90) REVERT: G 101 TRP cc_start: 0.8711 (p-90) cc_final: 0.7609 (p-90) REVERT: I 101 TRP cc_start: 0.8516 (p-90) cc_final: 0.8221 (p-90) REVERT: K 101 TRP cc_start: 0.8609 (p-90) cc_final: 0.7838 (p-90) REVERT: L 5 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9040 (tp30) REVERT: M 40 ASN cc_start: 0.6957 (m-40) cc_final: 0.6291 (m-40) REVERT: M 101 TRP cc_start: 0.8507 (p-90) cc_final: 0.7522 (p-90) REVERT: N 5 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8979 (tp30) REVERT: N 6 LEU cc_start: 0.9626 (mm) cc_final: 0.9378 (mm) REVERT: O 40 ASN cc_start: 0.7030 (m-40) cc_final: 0.6330 (m-40) REVERT: Q 101 TRP cc_start: 0.8586 (p-90) cc_final: 0.8113 (p-90) REVERT: R 48 GLU cc_start: 0.9441 (mm-30) cc_final: 0.9229 (mm-30) REVERT: S 43 TYR cc_start: 0.9138 (p90) cc_final: 0.8766 (p90) REVERT: S 101 TRP cc_start: 0.8586 (p-90) cc_final: 0.7669 (p-90) REVERT: T 3 LEU cc_start: 0.8763 (tt) cc_final: 0.8538 (tt) REVERT: U 101 TRP cc_start: 0.8669 (p-90) cc_final: 0.7770 (p-90) REVERT: V 5 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8869 (tp30) REVERT: V 6 LEU cc_start: 0.9664 (mm) cc_final: 0.9452 (mm) REVERT: V 48 GLU cc_start: 0.9464 (tp30) cc_final: 0.9186 (mm-30) REVERT: W 43 TYR cc_start: 0.9225 (p90) cc_final: 0.8923 (p90) REVERT: W 101 TRP cc_start: 0.8628 (p-90) cc_final: 0.7705 (p-90) REVERT: Y 101 TRP cc_start: 0.8607 (p-90) cc_final: 0.8192 (p-90) REVERT: Z 3 LEU cc_start: 0.8840 (tt) cc_final: 0.8599 (tp) REVERT: 0 40 ASN cc_start: 0.7050 (m-40) cc_final: 0.6304 (m-40) REVERT: 0 101 TRP cc_start: 0.8553 (p-90) cc_final: 0.7950 (p-90) REVERT: 1 5 GLU cc_start: 0.8679 (tt0) cc_final: 0.8219 (tp30) REVERT: 2 43 TYR cc_start: 0.9108 (p90) cc_final: 0.8890 (p90) REVERT: 2 101 TRP cc_start: 0.8602 (p-90) cc_final: 0.7608 (p-90) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2574 time to fit residues: 129.4420 Evaluate side-chains 197 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 ASN ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18585 Z= 0.271 Angle : 0.605 5.230 25335 Z= 0.329 Chirality : 0.043 0.230 3015 Planarity : 0.004 0.035 3225 Dihedral : 8.114 86.910 2565 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2385 helix: 1.54 (0.23), residues: 675 sheet: -0.70 (0.25), residues: 375 loop : -1.49 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 73 PHE 0.011 0.002 PHE T 24 TYR 0.014 0.002 TYR F 57 ARG 0.003 0.001 ARG X 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9305 (tp30) cc_final: 0.9025 (tp30) REVERT: a 13 ASP cc_start: 0.8658 (p0) cc_final: 0.8290 (p0) REVERT: a 101 TRP cc_start: 0.8700 (p-90) cc_final: 0.7588 (p-90) REVERT: C 101 TRP cc_start: 0.8671 (p-90) cc_final: 0.7644 (p-90) REVERT: E 13 ASP cc_start: 0.8725 (p0) cc_final: 0.8381 (p0) REVERT: E 101 TRP cc_start: 0.8617 (p-90) cc_final: 0.7594 (p-90) REVERT: G 13 ASP cc_start: 0.8728 (p0) cc_final: 0.8203 (p0) REVERT: G 101 TRP cc_start: 0.8839 (p-90) cc_final: 0.7715 (p-90) REVERT: I 101 TRP cc_start: 0.8646 (p-90) cc_final: 0.8260 (p-90) REVERT: K 13 ASP cc_start: 0.8934 (p0) cc_final: 0.8535 (p0) REVERT: K 43 TYR cc_start: 0.9096 (p90) cc_final: 0.8609 (p90) REVERT: K 101 TRP cc_start: 0.8615 (p-90) cc_final: 0.7691 (p-90) REVERT: N 5 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9036 (tp30) REVERT: N 6 LEU cc_start: 0.9636 (mm) cc_final: 0.9374 (mm) REVERT: P 5 GLU cc_start: 0.9322 (tp30) cc_final: 0.9106 (tp30) REVERT: Q 13 ASP cc_start: 0.8862 (p0) cc_final: 0.8385 (p0) REVERT: Q 101 TRP cc_start: 0.8677 (p-90) cc_final: 0.8157 (p-90) REVERT: S 101 TRP cc_start: 0.8666 (p-90) cc_final: 0.7593 (p-90) REVERT: T 3 LEU cc_start: 0.9063 (tt) cc_final: 0.8697 (tt) REVERT: T 5 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8829 (pt0) REVERT: U 13 ASP cc_start: 0.8717 (p0) cc_final: 0.8233 (p0) REVERT: U 101 TRP cc_start: 0.8689 (p-90) cc_final: 0.7781 (p-90) REVERT: W 101 TRP cc_start: 0.8621 (p-90) cc_final: 0.7765 (p-90) REVERT: X 3 LEU cc_start: 0.8791 (tt) cc_final: 0.8578 (tt) REVERT: X 5 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8760 (pt0) REVERT: Y 101 TRP cc_start: 0.8763 (p-90) cc_final: 0.8316 (p-90) REVERT: Z 5 GLU cc_start: 0.9274 (tp30) cc_final: 0.9008 (tp30) REVERT: 0 101 TRP cc_start: 0.8688 (p-90) cc_final: 0.8069 (p-90) REVERT: 1 5 GLU cc_start: 0.8833 (tt0) cc_final: 0.8346 (tp30) REVERT: 2 43 TYR cc_start: 0.9023 (p90) cc_final: 0.8497 (p90) REVERT: 2 101 TRP cc_start: 0.8769 (p-90) cc_final: 0.7733 (p-90) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2657 time to fit residues: 108.2904 Evaluate side-chains 192 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.0870 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 0.0670 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 ASN V 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18585 Z= 0.154 Angle : 0.530 6.144 25335 Z= 0.286 Chirality : 0.042 0.175 3015 Planarity : 0.003 0.034 3225 Dihedral : 7.987 88.296 2565 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 2385 helix: 2.06 (0.23), residues: 675 sheet: -0.70 (0.25), residues: 375 loop : -1.41 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 73 PHE 0.008 0.001 PHE P 24 TYR 0.012 0.001 TYR 1 57 ARG 0.002 0.000 ARG Z 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9232 (tp30) cc_final: 0.8824 (tp30) REVERT: a 13 ASP cc_start: 0.8684 (p0) cc_final: 0.8331 (p0) REVERT: C 3 LYS cc_start: 0.8125 (ptpp) cc_final: 0.7907 (mptt) REVERT: C 13 ASP cc_start: 0.8522 (p0) cc_final: 0.8134 (p0) REVERT: C 101 TRP cc_start: 0.8608 (p-90) cc_final: 0.7594 (p-90) REVERT: E 13 ASP cc_start: 0.8776 (p0) cc_final: 0.8414 (p0) REVERT: E 101 TRP cc_start: 0.8509 (p-90) cc_final: 0.7511 (p-90) REVERT: G 13 ASP cc_start: 0.8782 (p0) cc_final: 0.8246 (p0) REVERT: G 101 TRP cc_start: 0.8671 (p-90) cc_final: 0.7504 (p-90) REVERT: I 101 TRP cc_start: 0.8638 (p-90) cc_final: 0.8292 (p-90) REVERT: K 13 ASP cc_start: 0.8954 (p0) cc_final: 0.8538 (p0) REVERT: K 43 TYR cc_start: 0.9163 (p90) cc_final: 0.8651 (p90) REVERT: K 101 TRP cc_start: 0.8516 (p-90) cc_final: 0.7696 (p-90) REVERT: M 13 ASP cc_start: 0.8544 (p0) cc_final: 0.8198 (p0) REVERT: N 5 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8947 (tp30) REVERT: N 6 LEU cc_start: 0.9633 (mm) cc_final: 0.9323 (mm) REVERT: P 5 GLU cc_start: 0.9296 (tp30) cc_final: 0.8963 (tp30) REVERT: Q 13 ASP cc_start: 0.8893 (p0) cc_final: 0.8408 (p0) REVERT: Q 101 TRP cc_start: 0.8589 (p-90) cc_final: 0.8087 (p-90) REVERT: R 6 LEU cc_start: 0.9712 (mm) cc_final: 0.9480 (mm) REVERT: S 101 TRP cc_start: 0.8542 (p-90) cc_final: 0.7465 (p-90) REVERT: T 5 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8848 (pt0) REVERT: U 13 ASP cc_start: 0.8820 (p0) cc_final: 0.8320 (p0) REVERT: V 5 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8969 (tp30) REVERT: W 101 TRP cc_start: 0.8523 (p-90) cc_final: 0.7702 (p-90) REVERT: X 5 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8755 (pt0) REVERT: X 30 LYS cc_start: 0.9285 (mmtt) cc_final: 0.8557 (tmtt) REVERT: Y 101 TRP cc_start: 0.8639 (p-90) cc_final: 0.8194 (p-90) REVERT: Z 5 GLU cc_start: 0.9219 (tp30) cc_final: 0.8965 (tp30) REVERT: 0 43 TYR cc_start: 0.9253 (p90) cc_final: 0.9051 (p90) REVERT: 0 101 TRP cc_start: 0.8639 (p-90) cc_final: 0.8125 (p-90) REVERT: 1 5 GLU cc_start: 0.8703 (tt0) cc_final: 0.8277 (tp30) REVERT: 2 101 TRP cc_start: 0.8733 (p-90) cc_final: 0.7738 (p-90) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2812 time to fit residues: 110.1685 Evaluate side-chains 183 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 172 optimal weight: 0.0870 chunk 95 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.0010 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN B 42 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN J 42 ASN ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 42 ASN T 42 ASN V 42 ASN 0 64 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18585 Z= 0.136 Angle : 0.506 5.874 25335 Z= 0.271 Chirality : 0.041 0.151 3015 Planarity : 0.003 0.023 3225 Dihedral : 7.954 89.600 2565 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.31 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 2385 helix: 2.43 (0.23), residues: 675 sheet: -0.79 (0.25), residues: 375 loop : -1.48 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 73 PHE 0.010 0.001 PHE F 24 TYR 0.008 0.001 TYR G 26 ARG 0.003 0.001 ARG O 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9262 (tp30) cc_final: 0.8794 (tp30) REVERT: a 13 ASP cc_start: 0.8667 (p0) cc_final: 0.8293 (p0) REVERT: C 13 ASP cc_start: 0.8638 (p0) cc_final: 0.8290 (p0) REVERT: C 101 TRP cc_start: 0.8533 (p-90) cc_final: 0.7476 (p-90) REVERT: D 6 LEU cc_start: 0.9598 (mm) cc_final: 0.9392 (mm) REVERT: E 13 ASP cc_start: 0.8802 (p0) cc_final: 0.8406 (p0) REVERT: E 101 TRP cc_start: 0.8502 (p-90) cc_final: 0.7572 (p-90) REVERT: G 13 ASP cc_start: 0.8833 (p0) cc_final: 0.8358 (p0) REVERT: G 101 TRP cc_start: 0.8622 (p-90) cc_final: 0.7459 (p-90) REVERT: I 101 TRP cc_start: 0.8545 (p-90) cc_final: 0.8175 (p-90) REVERT: K 13 ASP cc_start: 0.8972 (p0) cc_final: 0.8558 (p0) REVERT: K 101 TRP cc_start: 0.8463 (p-90) cc_final: 0.7588 (p-90) REVERT: M 13 ASP cc_start: 0.8662 (p0) cc_final: 0.8309 (p0) REVERT: N 5 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8912 (tp30) REVERT: N 6 LEU cc_start: 0.9637 (mm) cc_final: 0.9359 (mm) REVERT: O 13 ASP cc_start: 0.8476 (p0) cc_final: 0.8187 (p0) REVERT: P 5 GLU cc_start: 0.9319 (tp30) cc_final: 0.8967 (tp30) REVERT: Q 13 ASP cc_start: 0.8993 (p0) cc_final: 0.8558 (p0) REVERT: Q 101 TRP cc_start: 0.8531 (p-90) cc_final: 0.8006 (p-90) REVERT: R 6 LEU cc_start: 0.9717 (mm) cc_final: 0.9507 (mm) REVERT: S 13 ASP cc_start: 0.8603 (p0) cc_final: 0.8243 (p0) REVERT: S 43 TYR cc_start: 0.8963 (p90) cc_final: 0.8577 (p90) REVERT: S 101 TRP cc_start: 0.8563 (p-90) cc_final: 0.7453 (p-90) REVERT: T 5 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8805 (pt0) REVERT: U 13 ASP cc_start: 0.8867 (p0) cc_final: 0.8371 (p0) REVERT: V 5 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8937 (tp30) REVERT: V 30 LYS cc_start: 0.9359 (mmtt) cc_final: 0.8705 (tmtt) REVERT: W 13 ASP cc_start: 0.8640 (p0) cc_final: 0.8325 (p0) REVERT: W 101 TRP cc_start: 0.8461 (p-90) cc_final: 0.7632 (p-90) REVERT: X 5 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8730 (pt0) REVERT: X 30 LYS cc_start: 0.9298 (mmtt) cc_final: 0.8626 (tmtt) REVERT: Y 9 MET cc_start: 0.9273 (tpp) cc_final: 0.9037 (tpt) REVERT: Y 101 TRP cc_start: 0.8566 (p-90) cc_final: 0.8151 (p-90) REVERT: Z 5 GLU cc_start: 0.9227 (tp30) cc_final: 0.8934 (tp30) REVERT: Z 30 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8742 (tmtt) REVERT: 0 43 TYR cc_start: 0.9292 (p90) cc_final: 0.9043 (p90) REVERT: 0 101 TRP cc_start: 0.8574 (p-90) cc_final: 0.8045 (p-90) REVERT: 1 5 GLU cc_start: 0.8683 (tt0) cc_final: 0.8231 (tp30) REVERT: 1 30 LYS cc_start: 0.9383 (mmtt) cc_final: 0.8662 (tmtt) REVERT: 2 101 TRP cc_start: 0.8654 (p-90) cc_final: 0.7661 (p-90) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2976 time to fit residues: 120.0270 Evaluate side-chains 172 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.0570 chunk 208 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 0.0570 chunk 121 optimal weight: 20.0000 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN B 42 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN J 42 ASN ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 42 ASN T 42 ASN V 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18585 Z= 0.220 Angle : 0.543 7.043 25335 Z= 0.294 Chirality : 0.042 0.157 3015 Planarity : 0.003 0.030 3225 Dihedral : 7.876 89.676 2565 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.73 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 2385 helix: 2.58 (0.23), residues: 675 sheet: -0.89 (0.24), residues: 375 loop : -1.58 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 73 PHE 0.008 0.001 PHE B 51 TYR 0.019 0.002 TYR C 43 ARG 0.002 0.000 ARG O 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9281 (tp30) cc_final: 0.8992 (tp30) REVERT: a 13 ASP cc_start: 0.8705 (p0) cc_final: 0.8308 (p0) REVERT: a 101 TRP cc_start: 0.8620 (p-90) cc_final: 0.7476 (p-90) REVERT: C 3 LYS cc_start: 0.8208 (ptpp) cc_final: 0.7966 (mptt) REVERT: C 13 ASP cc_start: 0.8780 (p0) cc_final: 0.8455 (p0) REVERT: C 101 TRP cc_start: 0.8566 (p-90) cc_final: 0.7533 (p-90) REVERT: E 13 ASP cc_start: 0.8908 (p0) cc_final: 0.8489 (p0) REVERT: E 101 TRP cc_start: 0.8584 (p-90) cc_final: 0.7602 (p-90) REVERT: G 13 ASP cc_start: 0.8805 (p0) cc_final: 0.8311 (p0) REVERT: G 101 TRP cc_start: 0.8695 (p-90) cc_final: 0.7536 (p-90) REVERT: I 13 ASP cc_start: 0.8730 (p0) cc_final: 0.8457 (p0) REVERT: I 101 TRP cc_start: 0.8618 (p-90) cc_final: 0.8195 (p-90) REVERT: K 13 ASP cc_start: 0.8924 (p0) cc_final: 0.8510 (p0) REVERT: K 101 TRP cc_start: 0.8536 (p-90) cc_final: 0.7593 (p-90) REVERT: M 13 ASP cc_start: 0.8751 (p0) cc_final: 0.8374 (p0) REVERT: N 5 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8878 (tp30) REVERT: N 6 LEU cc_start: 0.9646 (mm) cc_final: 0.9329 (mm) REVERT: O 13 ASP cc_start: 0.8686 (p0) cc_final: 0.8312 (p0) REVERT: P 5 GLU cc_start: 0.9325 (tp30) cc_final: 0.9104 (tp30) REVERT: Q 13 ASP cc_start: 0.9026 (p0) cc_final: 0.8609 (p0) REVERT: Q 43 TYR cc_start: 0.9393 (p90) cc_final: 0.9127 (p90) REVERT: Q 101 TRP cc_start: 0.8606 (p-90) cc_final: 0.8017 (p-90) REVERT: S 13 ASP cc_start: 0.8762 (p0) cc_final: 0.8387 (p0) REVERT: S 101 TRP cc_start: 0.8640 (p-90) cc_final: 0.7524 (p-90) REVERT: T 5 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8856 (pt0) REVERT: U 13 ASP cc_start: 0.8947 (p0) cc_final: 0.8501 (p0) REVERT: V 30 LYS cc_start: 0.9391 (mmtt) cc_final: 0.8814 (tmtt) REVERT: W 13 ASP cc_start: 0.8730 (p0) cc_final: 0.8386 (p0) REVERT: W 101 TRP cc_start: 0.8550 (p-90) cc_final: 0.7760 (p-90) REVERT: X 5 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8752 (pt0) REVERT: X 30 LYS cc_start: 0.9349 (mmtt) cc_final: 0.8697 (tmtt) REVERT: Y 101 TRP cc_start: 0.8655 (p-90) cc_final: 0.8255 (p-90) REVERT: Z 5 GLU cc_start: 0.9256 (tp30) cc_final: 0.9016 (tp30) REVERT: Z 30 LYS cc_start: 0.9379 (mmtt) cc_final: 0.8779 (tmtt) REVERT: 0 101 TRP cc_start: 0.8655 (p-90) cc_final: 0.8080 (p-90) REVERT: 1 5 GLU cc_start: 0.8747 (tt0) cc_final: 0.8265 (tp30) REVERT: 1 30 LYS cc_start: 0.9419 (mmtt) cc_final: 0.8708 (tmtt) REVERT: 2 43 TYR cc_start: 0.8840 (p90) cc_final: 0.8546 (p90) REVERT: 2 101 TRP cc_start: 0.8626 (p-90) cc_final: 0.7627 (p-90) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2555 time to fit residues: 90.8767 Evaluate side-chains 170 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN J 42 ASN ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN R 42 ASN T 42 ASN V 42 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18585 Z= 0.187 Angle : 0.547 6.421 25335 Z= 0.292 Chirality : 0.043 0.199 3015 Planarity : 0.003 0.028 3225 Dihedral : 7.555 86.531 2565 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 2385 helix: 2.60 (0.23), residues: 675 sheet: -0.80 (0.25), residues: 375 loop : -1.66 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 73 PHE 0.009 0.001 PHE F 24 TYR 0.017 0.001 TYR K 43 ARG 0.002 0.000 ARG Z 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9244 (tp30) cc_final: 0.8959 (tp30) REVERT: a 9 MET cc_start: 0.9323 (tpp) cc_final: 0.9069 (tpt) REVERT: a 13 ASP cc_start: 0.8773 (p0) cc_final: 0.8371 (p0) REVERT: a 101 TRP cc_start: 0.8618 (p-90) cc_final: 0.7564 (p-90) REVERT: C 13 ASP cc_start: 0.8839 (p0) cc_final: 0.8486 (p0) REVERT: C 101 TRP cc_start: 0.8605 (p-90) cc_final: 0.7621 (p-90) REVERT: E 13 ASP cc_start: 0.8911 (p0) cc_final: 0.8551 (p0) REVERT: G 13 ASP cc_start: 0.8802 (p0) cc_final: 0.8339 (p0) REVERT: G 101 TRP cc_start: 0.8583 (p-90) cc_final: 0.7428 (p-90) REVERT: I 13 ASP cc_start: 0.8790 (p0) cc_final: 0.8492 (p0) REVERT: I 101 TRP cc_start: 0.8533 (p-90) cc_final: 0.8149 (p-90) REVERT: K 13 ASP cc_start: 0.8954 (p0) cc_final: 0.8535 (p0) REVERT: K 101 TRP cc_start: 0.8431 (p-90) cc_final: 0.7544 (p-90) REVERT: L 5 GLU cc_start: 0.9320 (tp30) cc_final: 0.9102 (tp30) REVERT: M 13 ASP cc_start: 0.8817 (p0) cc_final: 0.8408 (p0) REVERT: M 101 TRP cc_start: 0.8583 (p-90) cc_final: 0.7381 (p-90) REVERT: N 5 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8847 (tp30) REVERT: N 6 LEU cc_start: 0.9642 (mm) cc_final: 0.9325 (mm) REVERT: O 13 ASP cc_start: 0.8788 (p0) cc_final: 0.8427 (p0) REVERT: P 5 GLU cc_start: 0.9336 (tp30) cc_final: 0.9074 (tp30) REVERT: Q 13 ASP cc_start: 0.9017 (p0) cc_final: 0.8606 (p0) REVERT: Q 43 TYR cc_start: 0.9343 (p90) cc_final: 0.9117 (p90) REVERT: Q 101 TRP cc_start: 0.8524 (p-90) cc_final: 0.7972 (p-90) REVERT: R 6 LEU cc_start: 0.9729 (mm) cc_final: 0.9497 (mm) REVERT: S 13 ASP cc_start: 0.8836 (p0) cc_final: 0.8508 (p0) REVERT: S 43 TYR cc_start: 0.9247 (p90) cc_final: 0.8987 (p90) REVERT: S 101 TRP cc_start: 0.8557 (p-90) cc_final: 0.7434 (p-90) REVERT: T 5 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8882 (pt0) REVERT: U 13 ASP cc_start: 0.8939 (p0) cc_final: 0.8472 (p0) REVERT: V 5 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8955 (tp30) REVERT: V 30 LYS cc_start: 0.9406 (mmtt) cc_final: 0.8821 (tmtt) REVERT: W 13 ASP cc_start: 0.8795 (p0) cc_final: 0.8435 (p0) REVERT: W 101 TRP cc_start: 0.8442 (p-90) cc_final: 0.7594 (p-90) REVERT: X 5 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8741 (pt0) REVERT: X 30 LYS cc_start: 0.9364 (mmtt) cc_final: 0.8693 (tmtt) REVERT: Y 13 ASP cc_start: 0.8411 (p0) cc_final: 0.8169 (p0) REVERT: Y 101 TRP cc_start: 0.8544 (p-90) cc_final: 0.8113 (p-90) REVERT: Z 5 GLU cc_start: 0.9248 (tp30) cc_final: 0.8979 (tp30) REVERT: Z 30 LYS cc_start: 0.9406 (mmtt) cc_final: 0.8806 (tmtt) REVERT: 0 43 TYR cc_start: 0.9351 (p90) cc_final: 0.9063 (p90) REVERT: 0 101 TRP cc_start: 0.8594 (p-90) cc_final: 0.8067 (p-90) REVERT: 1 5 GLU cc_start: 0.8722 (tt0) cc_final: 0.8218 (tp30) REVERT: 1 30 LYS cc_start: 0.9432 (mmtt) cc_final: 0.8675 (tmtt) REVERT: 2 13 ASP cc_start: 0.8433 (p0) cc_final: 0.8170 (p0) REVERT: 2 43 TYR cc_start: 0.8878 (p90) cc_final: 0.8675 (p90) REVERT: 2 101 TRP cc_start: 0.8625 (p-90) cc_final: 0.7644 (p-90) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2520 time to fit residues: 90.4081 Evaluate side-chains 170 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 0.0270 chunk 114 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 overall best weight: 2.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN R 42 ASN T 42 ASN V 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18585 Z= 0.212 Angle : 0.570 7.151 25335 Z= 0.303 Chirality : 0.043 0.210 3015 Planarity : 0.003 0.029 3225 Dihedral : 7.322 81.383 2565 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.14 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 2385 helix: 2.62 (0.23), residues: 675 sheet: -0.83 (0.25), residues: 375 loop : -1.75 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 73 PHE 0.007 0.001 PHE N 51 TYR 0.025 0.001 TYR C 43 ARG 0.002 0.000 ARG X 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9266 (tp30) cc_final: 0.8915 (tp30) REVERT: a 9 MET cc_start: 0.9388 (tpp) cc_final: 0.9149 (tpt) REVERT: a 13 ASP cc_start: 0.8806 (p0) cc_final: 0.8402 (p0) REVERT: a 43 TYR cc_start: 0.9271 (p90) cc_final: 0.8986 (p90) REVERT: a 101 TRP cc_start: 0.8642 (p-90) cc_final: 0.7632 (p-90) REVERT: C 13 ASP cc_start: 0.8866 (p0) cc_final: 0.8547 (p0) REVERT: C 101 TRP cc_start: 0.8668 (p-90) cc_final: 0.7607 (p-90) REVERT: E 13 ASP cc_start: 0.8899 (p0) cc_final: 0.8461 (p0) REVERT: E 101 TRP cc_start: 0.8562 (p-90) cc_final: 0.7390 (p-90) REVERT: G 9 MET cc_start: 0.9454 (mmm) cc_final: 0.9254 (tpt) REVERT: G 13 ASP cc_start: 0.8874 (p0) cc_final: 0.8474 (p0) REVERT: G 101 TRP cc_start: 0.8630 (p-90) cc_final: 0.7666 (p-90) REVERT: I 13 ASP cc_start: 0.8846 (p0) cc_final: 0.8539 (p0) REVERT: I 101 TRP cc_start: 0.8656 (p-90) cc_final: 0.8191 (p-90) REVERT: K 13 ASP cc_start: 0.8996 (p0) cc_final: 0.8600 (p0) REVERT: K 101 TRP cc_start: 0.8569 (p-90) cc_final: 0.7617 (p-90) REVERT: M 13 ASP cc_start: 0.8830 (p0) cc_final: 0.8424 (p0) REVERT: M 101 TRP cc_start: 0.8627 (p-90) cc_final: 0.7516 (p-90) REVERT: N 5 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8734 (pt0) REVERT: N 6 LEU cc_start: 0.9605 (mm) cc_final: 0.9397 (mm) REVERT: O 13 ASP cc_start: 0.8856 (p0) cc_final: 0.8496 (p0) REVERT: P 5 GLU cc_start: 0.9277 (tp30) cc_final: 0.9029 (tp30) REVERT: Q 13 ASP cc_start: 0.9016 (p0) cc_final: 0.8599 (p0) REVERT: Q 43 TYR cc_start: 0.9417 (p90) cc_final: 0.9129 (p90) REVERT: Q 101 TRP cc_start: 0.8601 (p-90) cc_final: 0.7903 (p-90) REVERT: S 13 ASP cc_start: 0.8888 (p0) cc_final: 0.8564 (p0) REVERT: S 43 TYR cc_start: 0.9389 (p90) cc_final: 0.9130 (p90) REVERT: S 101 TRP cc_start: 0.8511 (p-90) cc_final: 0.7248 (p-90) REVERT: U 13 ASP cc_start: 0.8959 (p0) cc_final: 0.8501 (p0) REVERT: U 101 TRP cc_start: 0.8624 (p-90) cc_final: 0.7524 (p-90) REVERT: V 30 LYS cc_start: 0.9433 (mmtt) cc_final: 0.8853 (tmtt) REVERT: W 13 ASP cc_start: 0.8913 (p0) cc_final: 0.8542 (p0) REVERT: W 101 TRP cc_start: 0.8582 (p-90) cc_final: 0.7859 (p-90) REVERT: X 5 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8812 (pt0) REVERT: X 30 LYS cc_start: 0.9400 (mmtt) cc_final: 0.8798 (tmtt) REVERT: Y 13 ASP cc_start: 0.8545 (p0) cc_final: 0.8276 (p0) REVERT: Y 101 TRP cc_start: 0.8609 (p-90) cc_final: 0.8218 (p-90) REVERT: Z 5 GLU cc_start: 0.9252 (tp30) cc_final: 0.8966 (tp30) REVERT: Z 30 LYS cc_start: 0.9429 (mmtt) cc_final: 0.8845 (tmtt) REVERT: 0 101 TRP cc_start: 0.8667 (p-90) cc_final: 0.8052 (p-90) REVERT: 1 30 LYS cc_start: 0.9451 (mmtt) cc_final: 0.8753 (tmtt) REVERT: 2 13 ASP cc_start: 0.8646 (p0) cc_final: 0.8396 (p0) REVERT: 2 101 TRP cc_start: 0.8555 (p-90) cc_final: 0.7497 (p-90) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2632 time to fit residues: 90.7403 Evaluate side-chains 166 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 203 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN ** R 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 ASN V 42 ASN W 64 ASN 0 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 18585 Z= 0.315 Angle : 0.622 7.160 25335 Z= 0.335 Chirality : 0.044 0.232 3015 Planarity : 0.004 0.031 3225 Dihedral : 7.411 77.849 2565 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2385 helix: 2.54 (0.23), residues: 675 sheet: -1.12 (0.24), residues: 375 loop : -1.83 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 73 PHE 0.010 0.001 PHE U 27 TYR 0.018 0.002 TYR K 43 ARG 0.002 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9301 (tp30) cc_final: 0.8959 (tp30) REVERT: a 13 ASP cc_start: 0.8904 (p0) cc_final: 0.8512 (p0) REVERT: a 101 TRP cc_start: 0.8656 (p-90) cc_final: 0.7748 (p-90) REVERT: C 13 ASP cc_start: 0.8896 (p0) cc_final: 0.8547 (p0) REVERT: C 101 TRP cc_start: 0.8737 (p-90) cc_final: 0.7732 (p-90) REVERT: E 13 ASP cc_start: 0.8871 (p0) cc_final: 0.8423 (p0) REVERT: E 101 TRP cc_start: 0.8680 (p-90) cc_final: 0.7583 (p-90) REVERT: G 13 ASP cc_start: 0.8946 (p0) cc_final: 0.8558 (p0) REVERT: G 101 TRP cc_start: 0.8739 (p-90) cc_final: 0.7752 (p-90) REVERT: I 13 ASP cc_start: 0.8913 (p0) cc_final: 0.8599 (p0) REVERT: I 101 TRP cc_start: 0.8660 (p-90) cc_final: 0.8115 (p-90) REVERT: K 13 ASP cc_start: 0.9028 (p0) cc_final: 0.8631 (p0) REVERT: K 43 TYR cc_start: 0.8858 (p90) cc_final: 0.8652 (p90) REVERT: K 101 TRP cc_start: 0.8630 (p-90) cc_final: 0.7661 (p-90) REVERT: M 13 ASP cc_start: 0.8912 (p0) cc_final: 0.8522 (p0) REVERT: M 101 TRP cc_start: 0.8637 (p-90) cc_final: 0.7551 (p-90) REVERT: N 5 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9013 (tp30) REVERT: N 6 LEU cc_start: 0.9611 (mm) cc_final: 0.9333 (mm) REVERT: O 13 ASP cc_start: 0.8932 (p0) cc_final: 0.8571 (p0) REVERT: P 5 GLU cc_start: 0.9331 (tp30) cc_final: 0.9076 (tp30) REVERT: Q 13 ASP cc_start: 0.9024 (p0) cc_final: 0.8608 (p0) REVERT: Q 43 TYR cc_start: 0.9397 (p90) cc_final: 0.8956 (p90) REVERT: Q 101 TRP cc_start: 0.8693 (p-90) cc_final: 0.7957 (p-90) REVERT: S 13 ASP cc_start: 0.8973 (p0) cc_final: 0.8681 (p0) REVERT: S 43 TYR cc_start: 0.9389 (p90) cc_final: 0.9188 (p90) REVERT: S 101 TRP cc_start: 0.8619 (p-90) cc_final: 0.7455 (p-90) REVERT: U 13 ASP cc_start: 0.9006 (p0) cc_final: 0.8512 (p0) REVERT: U 101 TRP cc_start: 0.8667 (p-90) cc_final: 0.7574 (p-90) REVERT: V 5 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8898 (tp30) REVERT: V 30 LYS cc_start: 0.9471 (mmtt) cc_final: 0.8909 (tmtt) REVERT: W 13 ASP cc_start: 0.8959 (p0) cc_final: 0.8604 (p0) REVERT: W 101 TRP cc_start: 0.8679 (p-90) cc_final: 0.7952 (p-90) REVERT: X 6 LEU cc_start: 0.9720 (mm) cc_final: 0.9497 (mm) REVERT: X 30 LYS cc_start: 0.9436 (mmtt) cc_final: 0.8831 (tmtt) REVERT: Y 13 ASP cc_start: 0.8696 (p0) cc_final: 0.8449 (p0) REVERT: Y 101 TRP cc_start: 0.8636 (p-90) cc_final: 0.8183 (p-90) REVERT: Z 5 GLU cc_start: 0.9290 (tp30) cc_final: 0.8989 (tp30) REVERT: Z 30 LYS cc_start: 0.9480 (mmtt) cc_final: 0.8920 (tmtt) REVERT: 0 101 TRP cc_start: 0.8670 (p-90) cc_final: 0.8019 (p-90) REVERT: 1 30 LYS cc_start: 0.9456 (mmtt) cc_final: 0.8819 (tmtt) REVERT: 2 13 ASP cc_start: 0.8711 (p0) cc_final: 0.8488 (p0) REVERT: 2 43 TYR cc_start: 0.9260 (p90) cc_final: 0.9024 (p90) REVERT: 2 101 TRP cc_start: 0.8594 (p-90) cc_final: 0.7490 (p-90) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2524 time to fit residues: 85.5812 Evaluate side-chains 161 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 158 optimal weight: 0.0870 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN I 60 ASN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN M 60 ASN N 42 ASN Q 40 ASN Q 60 ASN ** R 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 ASN V 42 ASN 0 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18585 Z= 0.214 Angle : 0.588 7.575 25335 Z= 0.312 Chirality : 0.043 0.196 3015 Planarity : 0.003 0.032 3225 Dihedral : 7.258 76.221 2565 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2385 helix: 2.62 (0.22), residues: 675 sheet: -1.12 (0.24), residues: 375 loop : -1.91 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 73 PHE 0.008 0.001 PHE D 51 TYR 0.020 0.001 TYR M 43 ARG 0.001 0.000 ARG X 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.693 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 5 GLU cc_start: 0.9274 (tp30) cc_final: 0.8914 (tp30) REVERT: a 9 MET cc_start: 0.9405 (tpp) cc_final: 0.9177 (tpt) REVERT: a 13 ASP cc_start: 0.8875 (p0) cc_final: 0.8481 (p0) REVERT: a 101 TRP cc_start: 0.8656 (p-90) cc_final: 0.7742 (p-90) REVERT: C 13 ASP cc_start: 0.8888 (p0) cc_final: 0.8549 (p0) REVERT: C 101 TRP cc_start: 0.8703 (p-90) cc_final: 0.7708 (p-90) REVERT: E 13 ASP cc_start: 0.8849 (p0) cc_final: 0.8401 (p0) REVERT: E 101 TRP cc_start: 0.8642 (p-90) cc_final: 0.7544 (p-90) REVERT: G 13 ASP cc_start: 0.8894 (p0) cc_final: 0.8438 (p0) REVERT: G 101 TRP cc_start: 0.8687 (p-90) cc_final: 0.7811 (p-90) REVERT: I 13 ASP cc_start: 0.8900 (p0) cc_final: 0.8595 (p0) REVERT: I 101 TRP cc_start: 0.8674 (p-90) cc_final: 0.8132 (p-90) REVERT: K 13 ASP cc_start: 0.9021 (p0) cc_final: 0.8633 (p0) REVERT: K 101 TRP cc_start: 0.8648 (p-90) cc_final: 0.7693 (p-90) REVERT: M 13 ASP cc_start: 0.8905 (p0) cc_final: 0.8511 (p0) REVERT: M 101 TRP cc_start: 0.8583 (p-90) cc_final: 0.7512 (p-90) REVERT: N 5 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8831 (pt0) REVERT: O 13 ASP cc_start: 0.8918 (p0) cc_final: 0.8571 (p0) REVERT: O 101 TRP cc_start: 0.8592 (p-90) cc_final: 0.8323 (p-90) REVERT: P 5 GLU cc_start: 0.9311 (tp30) cc_final: 0.9046 (tp30) REVERT: Q 13 ASP cc_start: 0.9029 (p0) cc_final: 0.8619 (p0) REVERT: Q 101 TRP cc_start: 0.8629 (p-90) cc_final: 0.7897 (p-90) REVERT: S 13 ASP cc_start: 0.8927 (p0) cc_final: 0.8553 (p0) REVERT: S 101 TRP cc_start: 0.8630 (p-90) cc_final: 0.7580 (p-90) REVERT: U 13 ASP cc_start: 0.8989 (p0) cc_final: 0.8494 (p0) REVERT: U 101 TRP cc_start: 0.8665 (p-90) cc_final: 0.7596 (p-90) REVERT: V 5 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8874 (tp30) REVERT: V 30 LYS cc_start: 0.9472 (mmtt) cc_final: 0.8919 (tmtt) REVERT: W 13 ASP cc_start: 0.8955 (p0) cc_final: 0.8627 (p0) REVERT: W 101 TRP cc_start: 0.8639 (p-90) cc_final: 0.7977 (p-90) REVERT: X 30 LYS cc_start: 0.9420 (mmtt) cc_final: 0.8822 (tmtt) REVERT: Y 13 ASP cc_start: 0.8658 (p0) cc_final: 0.8417 (p0) REVERT: Y 101 TRP cc_start: 0.8630 (p-90) cc_final: 0.8220 (p-90) REVERT: Z 3 LEU cc_start: 0.9365 (tp) cc_final: 0.9044 (tp) REVERT: Z 5 GLU cc_start: 0.9253 (tp30) cc_final: 0.8956 (tp30) REVERT: Z 30 LYS cc_start: 0.9490 (mmtt) cc_final: 0.8903 (tmtt) REVERT: 0 101 TRP cc_start: 0.8654 (p-90) cc_final: 0.8040 (p-90) REVERT: 1 30 LYS cc_start: 0.9464 (mmtt) cc_final: 0.8819 (tmtt) REVERT: 2 13 ASP cc_start: 0.8707 (p0) cc_final: 0.8470 (p0) REVERT: 2 101 TRP cc_start: 0.8552 (p-90) cc_final: 0.7539 (p-90) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2527 time to fit residues: 90.5042 Evaluate side-chains 166 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 0.0770 chunk 79 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 40 ASN a 60 ASN E 60 ASN I 60 ASN ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN M 40 ASN N 42 ASN Q 40 ASN Q 60 ASN R 42 ASN T 42 ASN V 42 ASN 0 40 ASN 0 60 ASN 2 60 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.041824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.034644 restraints weight = 109219.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036120 restraints weight = 61708.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037163 restraints weight = 40166.010| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18585 Z= 0.182 Angle : 0.567 8.621 25335 Z= 0.300 Chirality : 0.043 0.179 3015 Planarity : 0.003 0.032 3225 Dihedral : 7.085 75.022 2565 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % 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: -0.54 (0.18), residues: 2385 helix: 2.72 (0.23), residues: 675 sheet: -1.04 (0.25), residues: 375 loop : -1.92 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 73 PHE 0.008 0.001 PHE A 51 TYR 0.022 0.001 TYR C 43 ARG 0.002 0.000 ARG X 28 =============================================================================== Job complete usr+sys time: 3075.82 seconds wall clock time: 58 minutes 5.97 seconds (3485.97 seconds total)