Starting phenix.real_space_refine on Tue Aug 6 20:40:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/08_2024/7tgg_25881.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/08_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_25881/08_2024/7tgg_25881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/08_2024/7tgg_25881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/08_2024/7tgg_25881.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgg_25881/08_2024/7tgg_25881.cif" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 10.01, per 1000 atoms: 0.55 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: 7.43 Conformation dependent library (CDL) restraints added in 3.3 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: 1.51 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: 4.66 Time building geometry restraints manager: 8.09 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: 3411 1.46 - 1.57: 9264 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 E 15 " pdb=" CB THR E 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 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 ... (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: 7361 120.86 - 127.44: 6379 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: 19500 3.20 - 3.77: 28414 3.77 - 4.33: 39128 4.33 - 4.90: 62501 Nonbonded interactions: 149815 Sorted by model distance: nonbonded pdb=" OG1 THR O 15 " pdb=" NE2 GLN T 23 " model vdw 2.070 3.120 nonbonded pdb=" OG1 THR G 15 " pdb=" NE2 GLN L 23 " model vdw 2.070 3.120 nonbonded pdb=" OG1 THR K 15 " pdb=" NE2 GLN N 23 " model vdw 2.070 3.120 nonbonded pdb=" OG1 THR U 15 " pdb=" NE2 GLN Z 23 " model vdw 2.070 3.120 nonbonded pdb=" OG1 THR C 15 " pdb=" NE2 GLN H 23 " model vdw 2.070 3.120 ... (remaining 149810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 4.000 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.400 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.150 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.590 ------------------------------------------------------------------------------- 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 0.029 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 B 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 : 2.114 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: 0.8207 (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: 0.8091 (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: 0.7616 (p-90) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2727 time to fit residues: 154.8061 Evaluate side-chains 222 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.204 ------------------------------------------------------------------------------- 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: 5.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18585 Z= 0.270 Angle : 0.620 4.896 25335 Z= 0.348 Chirality : 0.044 0.152 3015 Planarity : 0.005 0.050 3225 Dihedral : 7.079 67.017 2565 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: -1.30 (0.18), residues: 2385 helix: 0.35 (0.21), residues: 675 sheet: -0.30 (0.23), residues: 375 loop : -1.73 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 73 PHE 0.020 0.002 PHE P 24 TYR 0.013 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 309 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 43 TYR cc_start: 0.9311 (p90) cc_final: 0.9029 (p90) REVERT: C 101 TRP cc_start: 0.8553 (p-90) cc_final: 0.7545 (p-90) REVERT: E 101 TRP cc_start: 0.8583 (p-90) cc_final: 0.7598 (p-90) REVERT: G 101 TRP cc_start: 0.8752 (p-90) cc_final: 0.7650 (p-90) REVERT: I 43 TYR cc_start: 0.9224 (p90) cc_final: 0.9011 (p90) REVERT: I 101 TRP cc_start: 0.8553 (p-90) cc_final: 0.8195 (p-90) REVERT: K 101 TRP cc_start: 0.8550 (p-90) cc_final: 0.7698 (p-90) REVERT: L 5 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9088 (tp30) REVERT: M 43 TYR cc_start: 0.9253 (p90) cc_final: 0.8587 (p90) REVERT: N 5 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9026 (tp30) REVERT: N 6 LEU cc_start: 0.9624 (mm) cc_final: 0.9381 (mm) REVERT: O 40 ASN cc_start: 0.7178 (m-40) cc_final: 0.6389 (m-40) REVERT: Q 43 TYR cc_start: 0.9311 (p90) cc_final: 0.9031 (p90) REVERT: Q 101 TRP cc_start: 0.8627 (p-90) cc_final: 0.8113 (p-90) REVERT: S 101 TRP cc_start: 0.8568 (p-90) cc_final: 0.7540 (p-90) REVERT: T 3 LEU cc_start: 0.8815 (tt) cc_final: 0.8595 (tt) REVERT: U 101 TRP cc_start: 0.8685 (p-90) cc_final: 0.7792 (p-90) REVERT: V 5 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8869 (tp30) REVERT: V 6 LEU cc_start: 0.9660 (mm) cc_final: 0.9449 (mm) REVERT: V 30 LYS cc_start: 0.9300 (mmtt) cc_final: 0.8700 (tmtt) REVERT: V 48 GLU cc_start: 0.9491 (tp30) cc_final: 0.9243 (mm-30) REVERT: W 43 TYR cc_start: 0.9238 (p90) cc_final: 0.8912 (p90) REVERT: W 101 TRP cc_start: 0.8666 (p-90) cc_final: 0.7803 (p-90) REVERT: Y 43 TYR cc_start: 0.9365 (p90) cc_final: 0.9136 (p90) REVERT: Y 101 TRP cc_start: 0.8680 (p-90) cc_final: 0.8268 (p-90) REVERT: Z 3 LEU cc_start: 0.8885 (tt) cc_final: 0.8670 (tp) REVERT: Z 30 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8673 (tmtt) REVERT: 0 40 ASN cc_start: 0.7154 (m-40) cc_final: 0.6388 (m-40) REVERT: 0 101 TRP cc_start: 0.8593 (p-90) cc_final: 0.7958 (p-90) REVERT: 1 5 GLU cc_start: 0.8789 (tt0) cc_final: 0.8305 (tp30) REVERT: 1 30 LYS cc_start: 0.9322 (mmtt) cc_final: 0.8607 (tmtt) REVERT: 2 101 TRP cc_start: 0.8635 (p-90) cc_final: 0.7627 (p-90) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2671 time to fit residues: 128.4556 Evaluate side-chains 199 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.055 ------------------------------------------------------------------------------- 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: 8.9990 chunk 181 optimal weight: 0.0770 chunk 148 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 overall best weight: 1.8942 ------------------------------------------------------------------------------- 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 T 42 ASN V 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18585 Z= 0.186 Angle : 0.552 5.836 25335 Z= 0.302 Chirality : 0.043 0.200 3015 Planarity : 0.004 0.036 3225 Dihedral : 6.500 61.072 2565 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -0.73 (0.18), residues: 2385 helix: 1.18 (0.22), residues: 675 sheet: -0.36 (0.25), residues: 375 loop : -1.45 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 73 PHE 0.011 0.001 PHE H 24 TYR 0.015 0.002 TYR K 43 ARG 0.003 0.001 ARG O 54 *********************** 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 291 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9229 (tp30) cc_final: 0.8886 (tp30) REVERT: a 13 ASP cc_start: 0.8479 (p0) cc_final: 0.8167 (p0) REVERT: C 101 TRP cc_start: 0.8525 (p-90) cc_final: 0.7481 (p-90) REVERT: D 6 LEU cc_start: 0.9601 (mm) cc_final: 0.9377 (mm) REVERT: E 13 ASP cc_start: 0.8597 (p0) cc_final: 0.8303 (p0) REVERT: E 101 TRP cc_start: 0.8494 (p-90) cc_final: 0.7534 (p-90) REVERT: G 13 ASP cc_start: 0.8534 (p0) cc_final: 0.8088 (p0) REVERT: G 101 TRP cc_start: 0.8717 (p-90) cc_final: 0.7630 (p-90) REVERT: I 101 TRP cc_start: 0.8577 (p-90) cc_final: 0.8237 (p-90) REVERT: K 13 ASP cc_start: 0.8749 (p0) cc_final: 0.8377 (p0) REVERT: K 101 TRP cc_start: 0.8476 (p-90) cc_final: 0.7630 (p-90) REVERT: M 43 TYR cc_start: 0.9291 (p90) cc_final: 0.9049 (p90) REVERT: N 5 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8979 (tp30) REVERT: N 6 LEU cc_start: 0.9609 (mm) cc_final: 0.9332 (mm) REVERT: P 5 GLU cc_start: 0.9268 (tp30) cc_final: 0.8990 (tp30) REVERT: Q 13 ASP cc_start: 0.8745 (p0) cc_final: 0.8318 (p0) REVERT: Q 48 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8694 (ttmm) REVERT: Q 101 TRP cc_start: 0.8582 (p-90) cc_final: 0.8050 (p-90) REVERT: S 101 TRP cc_start: 0.8574 (p-90) cc_final: 0.7569 (p-90) REVERT: T 3 LEU cc_start: 0.8950 (tt) cc_final: 0.8571 (tt) REVERT: U 13 ASP cc_start: 0.8664 (p0) cc_final: 0.8307 (p0) REVERT: V 30 LYS cc_start: 0.9281 (mmtt) cc_final: 0.8670 (tmtt) REVERT: W 48 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8671 (ttmm) REVERT: W 101 TRP cc_start: 0.8527 (p-90) cc_final: 0.7666 (p-90) REVERT: X 3 LEU cc_start: 0.8721 (tt) cc_final: 0.8510 (tt) REVERT: X 30 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8485 (tmtt) REVERT: Y 101 TRP cc_start: 0.8620 (p-90) cc_final: 0.8173 (p-90) REVERT: Z 3 LEU cc_start: 0.8950 (tt) cc_final: 0.8597 (tp) REVERT: Z 5 GLU cc_start: 0.9209 (tp30) cc_final: 0.8901 (tp30) REVERT: Z 30 LYS cc_start: 0.9306 (mmtt) cc_final: 0.8716 (tmtt) REVERT: 0 43 TYR cc_start: 0.9282 (p90) cc_final: 0.9016 (p90) REVERT: 0 101 TRP cc_start: 0.8600 (p-90) cc_final: 0.8055 (p-90) REVERT: 1 5 GLU cc_start: 0.8790 (tt0) cc_final: 0.8279 (tp30) REVERT: 1 30 LYS cc_start: 0.9349 (mmtt) cc_final: 0.8570 (tmtt) REVERT: 2 43 TYR cc_start: 0.9251 (p90) cc_final: 0.8786 (p90) REVERT: 2 48 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8849 (ttmm) REVERT: 2 101 TRP cc_start: 0.8684 (p-90) cc_final: 0.7711 (p-90) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3234 time to fit residues: 141.1363 Evaluate side-chains 192 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.923 ------------------------------------------------------------------------------- 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: 7.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 T 42 ASN V 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18585 Z= 0.259 Angle : 0.577 5.345 25335 Z= 0.314 Chirality : 0.043 0.177 3015 Planarity : 0.004 0.025 3225 Dihedral : 6.219 55.794 2565 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % 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: -0.59 (0.18), residues: 2385 helix: 1.68 (0.22), residues: 675 sheet: -0.52 (0.26), residues: 375 loop : -1.53 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 73 PHE 0.010 0.001 PHE N 51 TYR 0.017 0.002 TYR K 43 ARG 0.002 0.001 ARG X 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 241 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9273 (tp30) cc_final: 0.9013 (tp30) REVERT: a 13 ASP cc_start: 0.8678 (p0) cc_final: 0.8370 (p0) REVERT: a 101 TRP cc_start: 0.8642 (p-90) cc_final: 0.7554 (p-90) REVERT: C 101 TRP cc_start: 0.8697 (p-90) cc_final: 0.7651 (p-90) REVERT: E 13 ASP cc_start: 0.8731 (p0) cc_final: 0.8413 (p0) REVERT: E 101 TRP cc_start: 0.8620 (p-90) cc_final: 0.7617 (p-90) REVERT: G 13 ASP cc_start: 0.8736 (p0) cc_final: 0.8303 (p0) REVERT: G 101 TRP cc_start: 0.8746 (p-90) cc_final: 0.7657 (p-90) REVERT: I 43 TYR cc_start: 0.9508 (p90) cc_final: 0.9279 (p90) REVERT: I 101 TRP cc_start: 0.8624 (p-90) cc_final: 0.8193 (p-90) REVERT: K 13 ASP cc_start: 0.8892 (p0) cc_final: 0.8558 (p0) REVERT: K 43 TYR cc_start: 0.9372 (p90) cc_final: 0.8885 (p90) REVERT: K 101 TRP cc_start: 0.8595 (p-90) cc_final: 0.7640 (p-90) REVERT: L 5 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9148 (tp30) REVERT: N 5 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8947 (tp30) REVERT: N 6 LEU cc_start: 0.9660 (mm) cc_final: 0.9350 (mm) REVERT: P 5 GLU cc_start: 0.9325 (tp30) cc_final: 0.9110 (tp30) REVERT: Q 13 ASP cc_start: 0.8848 (p0) cc_final: 0.8443 (p0) REVERT: Q 43 TYR cc_start: 0.9516 (p90) cc_final: 0.9300 (p90) REVERT: Q 101 TRP cc_start: 0.8681 (p-90) cc_final: 0.8101 (p-90) REVERT: R 6 LEU cc_start: 0.9763 (mm) cc_final: 0.9517 (mm) REVERT: S 101 TRP cc_start: 0.8658 (p-90) cc_final: 0.7558 (p-90) REVERT: U 13 ASP cc_start: 0.8817 (p0) cc_final: 0.8423 (p0) REVERT: V 5 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9013 (tp30) REVERT: V 30 LYS cc_start: 0.9352 (mmtt) cc_final: 0.8730 (tmtt) REVERT: W 101 TRP cc_start: 0.8646 (p-90) cc_final: 0.7812 (p-90) REVERT: X 3 LEU cc_start: 0.9038 (tt) cc_final: 0.8811 (tt) REVERT: X 6 LEU cc_start: 0.9759 (mm) cc_final: 0.9539 (mm) REVERT: X 30 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8619 (tmtt) REVERT: Y 101 TRP cc_start: 0.8757 (p-90) cc_final: 0.8339 (p-90) REVERT: Z 5 GLU cc_start: 0.9261 (tp30) cc_final: 0.8978 (tp30) REVERT: Z 30 LYS cc_start: 0.9383 (mmtt) cc_final: 0.8844 (tmtt) REVERT: 0 101 TRP cc_start: 0.8714 (p-90) cc_final: 0.8088 (p-90) REVERT: 1 5 GLU cc_start: 0.8710 (tt0) cc_final: 0.8275 (tp30) REVERT: 1 30 LYS cc_start: 0.9369 (mmtt) cc_final: 0.8677 (tmtt) REVERT: 2 43 TYR cc_start: 0.9285 (p90) cc_final: 0.8753 (p90) REVERT: 2 101 TRP cc_start: 0.8772 (p-90) cc_final: 0.7731 (p-90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2706 time to fit residues: 103.2911 Evaluate side-chains 183 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.024 ------------------------------------------------------------------------------- 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: 7.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18585 Z= 0.187 Angle : 0.542 4.838 25335 Z= 0.295 Chirality : 0.043 0.158 3015 Planarity : 0.003 0.025 3225 Dihedral : 5.793 50.638 2565 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.44 (0.19), residues: 2385 helix: 2.04 (0.23), residues: 675 sheet: -0.50 (0.27), residues: 375 loop : -1.54 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 73 PHE 0.007 0.001 PHE A 51 TYR 0.018 0.002 TYR C 43 ARG 0.003 0.000 ARG P 41 *********************** 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 227 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9232 (tp30) cc_final: 0.8971 (tp30) REVERT: a 13 ASP cc_start: 0.8722 (p0) cc_final: 0.8416 (p0) REVERT: C 101 TRP cc_start: 0.8597 (p-90) cc_final: 0.7609 (p-90) REVERT: E 13 ASP cc_start: 0.8763 (p0) cc_final: 0.8456 (p0) REVERT: G 13 ASP cc_start: 0.8760 (p0) cc_final: 0.8333 (p0) REVERT: G 101 TRP cc_start: 0.8621 (p-90) cc_final: 0.7500 (p-90) REVERT: I 101 TRP cc_start: 0.8577 (p-90) cc_final: 0.8173 (p-90) REVERT: K 13 ASP cc_start: 0.8905 (p0) cc_final: 0.8577 (p0) REVERT: K 43 TYR cc_start: 0.9334 (p90) cc_final: 0.8934 (p90) REVERT: K 101 TRP cc_start: 0.8460 (p-90) cc_final: 0.7549 (p-90) REVERT: L 5 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8993 (tp30) REVERT: M 101 TRP cc_start: 0.8586 (p-90) cc_final: 0.7328 (p-90) REVERT: N 5 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8864 (tp30) REVERT: N 6 LEU cc_start: 0.9616 (mm) cc_final: 0.9343 (mm) REVERT: P 5 GLU cc_start: 0.9336 (tp30) cc_final: 0.9099 (tp30) REVERT: Q 13 ASP cc_start: 0.8864 (p0) cc_final: 0.8441 (p0) REVERT: Q 101 TRP cc_start: 0.8574 (p-90) cc_final: 0.8054 (p-90) REVERT: R 6 LEU cc_start: 0.9773 (mm) cc_final: 0.9556 (mm) REVERT: S 43 TYR cc_start: 0.9421 (p90) cc_final: 0.8776 (p90) REVERT: S 101 TRP cc_start: 0.8536 (p-90) cc_final: 0.7399 (p-90) REVERT: U 13 ASP cc_start: 0.8879 (p0) cc_final: 0.8510 (p0) REVERT: V 30 LYS cc_start: 0.9374 (mmtt) cc_final: 0.8770 (tmtt) REVERT: W 101 TRP cc_start: 0.8476 (p-90) cc_final: 0.7640 (p-90) REVERT: X 3 LEU cc_start: 0.9060 (tt) cc_final: 0.8786 (tt) REVERT: X 30 LYS cc_start: 0.9338 (mmtt) cc_final: 0.8656 (tmtt) REVERT: Y 101 TRP cc_start: 0.8613 (p-90) cc_final: 0.8175 (p-90) REVERT: Z 5 GLU cc_start: 0.9253 (tp30) cc_final: 0.8994 (tp30) REVERT: Z 30 LYS cc_start: 0.9373 (mmtt) cc_final: 0.8861 (tmtt) REVERT: 0 101 TRP cc_start: 0.8627 (p-90) cc_final: 0.8077 (p-90) REVERT: 1 5 GLU cc_start: 0.8710 (tt0) cc_final: 0.8245 (tp30) REVERT: 1 30 LYS cc_start: 0.9374 (mmtt) cc_final: 0.8673 (tmtt) REVERT: 2 43 TYR cc_start: 0.9101 (p90) cc_final: 0.8834 (p90) REVERT: 2 101 TRP cc_start: 0.8666 (p-90) cc_final: 0.7640 (p-90) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2471 time to fit residues: 91.2441 Evaluate side-chains 180 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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: 5.9990 chunk 208 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN R 42 ASN T 42 ASN V 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18585 Z= 0.198 Angle : 0.541 5.627 25335 Z= 0.293 Chirality : 0.042 0.176 3015 Planarity : 0.003 0.021 3225 Dihedral : 5.554 47.188 2565 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -0.48 (0.19), residues: 2385 helix: 2.19 (0.23), residues: 675 sheet: -0.53 (0.27), residues: 375 loop : -1.68 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 73 PHE 0.009 0.001 PHE F 24 TYR 0.021 0.001 TYR I 43 ARG 0.003 0.000 ARG R 41 *********************** 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 220 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9254 (tp30) cc_final: 0.8968 (tp30) REVERT: a 13 ASP cc_start: 0.8748 (p0) cc_final: 0.8441 (p0) REVERT: C 101 TRP cc_start: 0.8608 (p-90) cc_final: 0.7587 (p-90) REVERT: E 13 ASP cc_start: 0.8738 (p0) cc_final: 0.8423 (p0) REVERT: G 13 ASP cc_start: 0.8798 (p0) cc_final: 0.8364 (p0) REVERT: G 101 TRP cc_start: 0.8629 (p-90) cc_final: 0.7559 (p-90) REVERT: I 101 TRP cc_start: 0.8605 (p-90) cc_final: 0.8171 (p-90) REVERT: K 13 ASP cc_start: 0.8859 (p0) cc_final: 0.8517 (p0) REVERT: K 43 TYR cc_start: 0.9289 (p90) cc_final: 0.9049 (p90) REVERT: K 101 TRP cc_start: 0.8507 (p-90) cc_final: 0.7556 (p-90) REVERT: L 5 GLU cc_start: 0.9373 (mm-30) cc_final: 0.8970 (tp30) REVERT: M 101 TRP cc_start: 0.8529 (p-90) cc_final: 0.7343 (p-90) REVERT: N 5 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8883 (tp30) REVERT: N 6 LEU cc_start: 0.9626 (mm) cc_final: 0.9304 (mm) REVERT: P 5 GLU cc_start: 0.9332 (tp30) cc_final: 0.9068 (tp30) REVERT: Q 13 ASP cc_start: 0.8907 (p0) cc_final: 0.8510 (p0) REVERT: Q 101 TRP cc_start: 0.8576 (p-90) cc_final: 0.7949 (p-90) REVERT: R 6 LEU cc_start: 0.9776 (mm) cc_final: 0.9569 (mm) REVERT: S 43 TYR cc_start: 0.9399 (p90) cc_final: 0.8900 (p90) REVERT: S 101 TRP cc_start: 0.8535 (p-90) cc_final: 0.7332 (p-90) REVERT: U 13 ASP cc_start: 0.8897 (p0) cc_final: 0.8525 (p0) REVERT: V 5 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9005 (tp30) REVERT: V 30 LYS cc_start: 0.9365 (mmtt) cc_final: 0.8834 (tmtt) REVERT: W 101 TRP cc_start: 0.8493 (p-90) cc_final: 0.7721 (p-90) REVERT: X 30 LYS cc_start: 0.9329 (mmtt) cc_final: 0.8666 (tmtt) REVERT: Y 13 ASP cc_start: 0.8415 (p0) cc_final: 0.8130 (p0) REVERT: Y 101 TRP cc_start: 0.8600 (p-90) cc_final: 0.8181 (p-90) REVERT: Z 5 GLU cc_start: 0.9266 (tp30) cc_final: 0.9001 (tp30) REVERT: Z 30 LYS cc_start: 0.9373 (mmtt) cc_final: 0.8860 (tmtt) REVERT: 0 101 TRP cc_start: 0.8619 (p-90) cc_final: 0.8071 (p-90) REVERT: 1 3 LEU cc_start: 0.8850 (tt) cc_final: 0.8626 (tt) REVERT: 1 5 GLU cc_start: 0.8699 (tt0) cc_final: 0.8218 (tp30) REVERT: 1 30 LYS cc_start: 0.9391 (mmtt) cc_final: 0.8713 (tmtt) REVERT: 2 43 TYR cc_start: 0.9168 (p90) cc_final: 0.8916 (p90) REVERT: 2 101 TRP cc_start: 0.8637 (p-90) cc_final: 0.7682 (p-90) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2494 time to fit residues: 89.0038 Evaluate side-chains 176 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.173 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 231 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 0.0980 chunk 106 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN R 42 ASN T 42 ASN V 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18585 Z= 0.164 Angle : 0.543 6.653 25335 Z= 0.289 Chirality : 0.043 0.189 3015 Planarity : 0.003 0.023 3225 Dihedral : 5.252 42.692 2565 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % 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: -0.47 (0.18), residues: 2385 helix: 2.27 (0.23), residues: 675 sheet: -0.46 (0.27), residues: 375 loop : -1.75 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 73 PHE 0.008 0.001 PHE A 51 TYR 0.022 0.001 TYR C 43 ARG 0.002 0.000 ARG P 41 *********************** 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 225 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8942 (tt) cc_final: 0.8545 (tt) REVERT: A 5 GLU cc_start: 0.9236 (tp30) cc_final: 0.8964 (tp30) REVERT: a 13 ASP cc_start: 0.8775 (p0) cc_final: 0.8461 (p0) REVERT: a 101 TRP cc_start: 0.8610 (p-90) cc_final: 0.7562 (p-90) REVERT: C 101 TRP cc_start: 0.8603 (p-90) cc_final: 0.7597 (p-90) REVERT: E 13 ASP cc_start: 0.8773 (p0) cc_final: 0.8443 (p0) REVERT: G 9 MET cc_start: 0.9471 (mmm) cc_final: 0.9261 (tpt) REVERT: G 13 ASP cc_start: 0.8725 (p0) cc_final: 0.8318 (p0) REVERT: G 101 TRP cc_start: 0.8573 (p-90) cc_final: 0.7534 (p-90) REVERT: I 43 TYR cc_start: 0.9398 (p90) cc_final: 0.8976 (p90) REVERT: I 101 TRP cc_start: 0.8577 (p-90) cc_final: 0.8146 (p-90) REVERT: K 13 ASP cc_start: 0.8802 (p0) cc_final: 0.8481 (p0) REVERT: K 101 TRP cc_start: 0.8459 (p-90) cc_final: 0.7508 (p-90) REVERT: L 5 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8899 (tp30) REVERT: M 101 TRP cc_start: 0.8536 (p-90) cc_final: 0.7401 (p-90) REVERT: N 5 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8698 (pt0) REVERT: N 6 LEU cc_start: 0.9603 (mm) cc_final: 0.9375 (mm) REVERT: P 5 GLU cc_start: 0.9317 (tp30) cc_final: 0.9053 (tp30) REVERT: Q 13 ASP cc_start: 0.8891 (p0) cc_final: 0.8440 (p0) REVERT: Q 101 TRP cc_start: 0.8541 (p-90) cc_final: 0.7870 (p-90) REVERT: R 6 LEU cc_start: 0.9729 (mm) cc_final: 0.9491 (mm) REVERT: S 13 ASP cc_start: 0.8694 (p0) cc_final: 0.8394 (p0) REVERT: S 43 TYR cc_start: 0.9347 (p90) cc_final: 0.8956 (p90) REVERT: S 101 TRP cc_start: 0.8520 (p-90) cc_final: 0.7314 (p-90) REVERT: U 13 ASP cc_start: 0.8879 (p0) cc_final: 0.8549 (p0) REVERT: V 5 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8885 (tp30) REVERT: V 30 LYS cc_start: 0.9350 (mmtt) cc_final: 0.8779 (tmtt) REVERT: W 13 ASP cc_start: 0.8639 (p0) cc_final: 0.8410 (p0) REVERT: W 101 TRP cc_start: 0.8474 (p-90) cc_final: 0.7749 (p-90) REVERT: X 30 LYS cc_start: 0.9308 (mmtt) cc_final: 0.8676 (tmtt) REVERT: Y 9 MET cc_start: 0.9508 (tpp) cc_final: 0.9278 (tpt) REVERT: Y 101 TRP cc_start: 0.8546 (p-90) cc_final: 0.8158 (p-90) REVERT: Z 5 GLU cc_start: 0.9273 (tp30) cc_final: 0.9017 (tp30) REVERT: Z 30 LYS cc_start: 0.9348 (mmtt) cc_final: 0.8865 (tmtt) REVERT: Z 48 GLU cc_start: 0.9642 (tp30) cc_final: 0.9408 (tp30) REVERT: 0 101 TRP cc_start: 0.8556 (p-90) cc_final: 0.7966 (p-90) REVERT: 1 3 LEU cc_start: 0.8942 (tt) cc_final: 0.8726 (tt) REVERT: 1 5 GLU cc_start: 0.8686 (tt0) cc_final: 0.8179 (tp30) REVERT: 1 6 LEU cc_start: 0.9609 (mm) cc_final: 0.9402 (mm) REVERT: 1 30 LYS cc_start: 0.9392 (mmtt) cc_final: 0.8725 (tmtt) REVERT: 2 43 TYR cc_start: 0.9136 (p90) cc_final: 0.8928 (p90) REVERT: 2 101 TRP cc_start: 0.8597 (p-90) cc_final: 0.7601 (p-90) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2572 time to fit residues: 94.1736 Evaluate side-chains 175 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN R 42 ASN T 42 ASN V 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18585 Z= 0.315 Angle : 0.627 7.409 25335 Z= 0.336 Chirality : 0.046 0.217 3015 Planarity : 0.004 0.027 3225 Dihedral : 5.611 44.897 2565 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.14 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -0.69 (0.18), residues: 2385 helix: 2.23 (0.22), residues: 675 sheet: -0.73 (0.26), residues: 375 loop : -1.93 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 73 PHE 0.010 0.001 PHE M 56 TYR 0.012 0.002 TYR Q 43 ARG 0.002 0.000 ARG O 54 *********************** 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 : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9289 (tp30) cc_final: 0.9008 (tp30) REVERT: a 13 ASP cc_start: 0.8798 (p0) cc_final: 0.8478 (p0) REVERT: a 101 TRP cc_start: 0.8657 (p-90) cc_final: 0.7765 (p-90) REVERT: C 101 TRP cc_start: 0.8673 (p-90) cc_final: 0.7626 (p-90) REVERT: E 13 ASP cc_start: 0.8796 (p0) cc_final: 0.8467 (p0) REVERT: E 101 TRP cc_start: 0.8628 (p-90) cc_final: 0.7501 (p-90) REVERT: G 13 ASP cc_start: 0.8752 (p0) cc_final: 0.8363 (p0) REVERT: G 101 TRP cc_start: 0.8724 (p-90) cc_final: 0.7760 (p-90) REVERT: I 101 TRP cc_start: 0.8701 (p-90) cc_final: 0.8144 (p-90) REVERT: K 13 ASP cc_start: 0.8862 (p0) cc_final: 0.8509 (p0) REVERT: K 101 TRP cc_start: 0.8640 (p-90) cc_final: 0.7543 (p-90) REVERT: M 101 TRP cc_start: 0.8675 (p-90) cc_final: 0.7554 (p-90) REVERT: N 5 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9054 (tp30) REVERT: N 6 LEU cc_start: 0.9622 (mm) cc_final: 0.9377 (mm) REVERT: P 5 GLU cc_start: 0.9347 (tp30) cc_final: 0.9071 (tp30) REVERT: Q 13 ASP cc_start: 0.8886 (p0) cc_final: 0.8521 (p0) REVERT: Q 101 TRP cc_start: 0.8637 (p-90) cc_final: 0.7887 (p-90) REVERT: R 6 LEU cc_start: 0.9748 (mm) cc_final: 0.9507 (mm) REVERT: S 13 ASP cc_start: 0.8789 (p0) cc_final: 0.8516 (p0) REVERT: S 101 TRP cc_start: 0.8544 (p-90) cc_final: 0.7346 (p-90) REVERT: U 13 ASP cc_start: 0.8883 (p0) cc_final: 0.8531 (p0) REVERT: U 101 TRP cc_start: 0.8679 (p-90) cc_final: 0.7598 (p-90) REVERT: V 30 LYS cc_start: 0.9443 (mmtt) cc_final: 0.8905 (tmtt) REVERT: W 13 ASP cc_start: 0.8779 (p0) cc_final: 0.8508 (p0) REVERT: W 101 TRP cc_start: 0.8649 (p-90) cc_final: 0.7952 (p-90) REVERT: X 30 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8786 (tmtt) REVERT: Y 101 TRP cc_start: 0.8584 (p-90) cc_final: 0.8154 (p-90) REVERT: Z 5 GLU cc_start: 0.9292 (tp30) cc_final: 0.9000 (tp30) REVERT: Z 30 LYS cc_start: 0.9442 (mmtt) cc_final: 0.8956 (tmtt) REVERT: 0 101 TRP cc_start: 0.8608 (p-90) cc_final: 0.7920 (p-90) REVERT: 1 30 LYS cc_start: 0.9452 (mmtt) cc_final: 0.8811 (tmtt) REVERT: 2 101 TRP cc_start: 0.8628 (p-90) cc_final: 0.7616 (p-90) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2512 time to fit residues: 86.8914 Evaluate side-chains 165 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5905 > 50: distance: 38 - 39: 41.327 distance: 39 - 40: 56.757 distance: 45 - 46: 57.506 distance: 45 - 47: 40.286 distance: 47 - 48: 43.159 distance: 48 - 49: 25.619 distance: 48 - 51: 47.591 distance: 49 - 50: 56.095 distance: 49 - 56: 38.806 distance: 52 - 53: 39.241 distance: 53 - 54: 41.437 distance: 56 - 57: 57.610 distance: 57 - 58: 55.075 distance: 57 - 60: 57.299 distance: 58 - 59: 57.469 distance: 58 - 64: 57.580 distance: 60 - 61: 40.697 distance: 64 - 65: 55.568 distance: 64 - 70: 56.564 distance: 65 - 66: 56.938 distance: 66 - 67: 57.579 distance: 66 - 71: 39.377 distance: 69 - 70: 57.924 distance: 71 - 72: 40.412 distance: 72 - 73: 39.747 distance: 72 - 75: 56.851 distance: 73 - 74: 38.839 distance: 73 - 78: 40.887 distance: 75 - 77: 56.648 distance: 78 - 79: 40.350 distance: 80 - 81: 39.237 distance: 80 - 85: 41.311 distance: 82 - 83: 56.366 distance: 85 - 86: 38.838 distance: 86 - 89: 13.536 distance: 87 - 88: 57.579 distance: 87 - 92: 40.456 distance: 89 - 90: 11.608 distance: 89 - 91: 11.071 distance: 92 - 93: 41.417 distance: 93 - 94: 41.232 distance: 93 - 96: 57.333 distance: 94 - 95: 55.953 distance: 94 - 100: 34.117 distance: 97 - 98: 56.229 distance: 98 - 99: 57.201