Starting phenix.real_space_refine on Sat Mar 16 08:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znh_11311/03_2024/6znh_11311.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znh_11311/03_2024/6znh_11311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znh_11311/03_2024/6znh_11311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znh_11311/03_2024/6znh_11311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znh_11311/03_2024/6znh_11311.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6znh_11311/03_2024/6znh_11311.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 3 Type Number sf(0) Gaussians C 8970 2.51 5 N 2346 2.21 5 O 2875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "J PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "K PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "L PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "M PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "N PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "O PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 80": "NH1" <-> "NH2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "Q PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 80": "NH1" <-> "NH2" Residue "R PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "S PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "T PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 80": "NH1" <-> "NH2" Residue "U PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "V PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 80": "NH1" <-> "NH2" Residue "W PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 80": "NH1" <-> "NH2" 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: 14191 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "B" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "C" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "D" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "E" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "G" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "H" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "I" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "J" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "K" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "M" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Time building chain proxies: 7.35, per 1000 atoms: 0.52 Number of scatterers: 14191 At special positions: 0 Unit cell: (98.1, 99.19, 173.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2875 8.00 N 2346 7.00 C 8970 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: 6.01 Conformation dependent library (CDL) restraints added in 2.7 seconds 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3542 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 0 sheets defined 86.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 75 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 76 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 22 through 35 Processing helix chain 'E' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE E 75 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 22 through 35 Processing helix chain 'F' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE G 75 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE G 76 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 22 through 35 Processing helix chain 'H' and resid 40 through 76 removed outlier: 3.985A pdb=" N ALA H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE H 75 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE H 76 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'I' and resid 7 through 20 Processing helix chain 'I' and resid 22 through 35 Processing helix chain 'I' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 76 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'J' and resid 7 through 20 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE J 75 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE J 76 " --> pdb=" O ASP J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 79 No H-bonds generated for 'chain 'J' and resid 77 through 79' Processing helix chain 'K' and resid 7 through 20 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE L 75 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 79 No H-bonds generated for 'chain 'L' and resid 77 through 79' Processing helix chain 'M' and resid 7 through 20 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA M 74 " --> pdb=" O ASP M 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE M 75 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE M 76 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 79 No H-bonds generated for 'chain 'M' and resid 77 through 79' Processing helix chain 'N' and resid 7 through 20 Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE N 75 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 79 No H-bonds generated for 'chain 'N' and resid 77 through 79' Processing helix chain 'O' and resid 7 through 20 Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE O 75 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE O 76 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 79 No H-bonds generated for 'chain 'O' and resid 77 through 79' Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'P' and resid 22 through 35 Processing helix chain 'P' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE P 75 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE P 76 " --> pdb=" O ASP P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 79 No H-bonds generated for 'chain 'P' and resid 77 through 79' Processing helix chain 'Q' and resid 7 through 20 Processing helix chain 'Q' and resid 22 through 35 Processing helix chain 'Q' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA Q 74 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE Q 75 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE Q 76 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 79 No H-bonds generated for 'chain 'Q' and resid 77 through 79' Processing helix chain 'R' and resid 7 through 20 Processing helix chain 'R' and resid 22 through 35 Processing helix chain 'R' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA R 74 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE R 75 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE R 76 " --> pdb=" O ASP R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 79 No H-bonds generated for 'chain 'R' and resid 77 through 79' Processing helix chain 'S' and resid 7 through 20 Processing helix chain 'S' and resid 22 through 35 Processing helix chain 'S' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA S 74 " --> pdb=" O ASP S 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE S 75 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE S 76 " --> pdb=" O ASP S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 79 No H-bonds generated for 'chain 'S' and resid 77 through 79' Processing helix chain 'T' and resid 7 through 20 Processing helix chain 'T' and resid 22 through 35 Processing helix chain 'T' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA T 74 " --> pdb=" O ASP T 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE T 75 " --> pdb=" O ILE T 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE T 76 " --> pdb=" O ASP T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 79 No H-bonds generated for 'chain 'T' and resid 77 through 79' Processing helix chain 'U' and resid 7 through 20 Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'U' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA U 74 " --> pdb=" O ASP U 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE U 75 " --> pdb=" O ILE U 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE U 76 " --> pdb=" O ASP U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 79 No H-bonds generated for 'chain 'U' and resid 77 through 79' Processing helix chain 'V' and resid 7 through 20 Processing helix chain 'V' and resid 22 through 35 Processing helix chain 'V' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA V 74 " --> pdb=" O ASP V 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE V 75 " --> pdb=" O ILE V 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE V 76 " --> pdb=" O ASP V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 79 No H-bonds generated for 'chain 'V' and resid 77 through 79' Processing helix chain 'W' and resid 7 through 20 Processing helix chain 'W' and resid 22 through 35 Processing helix chain 'W' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA W 74 " --> pdb=" O ASP W 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE W 75 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE W 76 " --> pdb=" O ASP W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 79 No H-bonds generated for 'chain 'W' and resid 77 through 79' 1150 hydrogen bonds defined for protein. 3450 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: 4.21 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2530 1.29 - 1.35: 2162 1.35 - 1.42: 1403 1.42 - 1.48: 2092 1.48 - 1.54: 6257 Bond restraints: 14444 Sorted by residual: bond pdb=" C ARG K 58 " pdb=" O ARG K 58 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.47e-01 bond pdb=" C ARG T 58 " pdb=" O ARG T 58 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.45e-01 bond pdb=" C ARG A 58 " pdb=" O ARG A 58 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.35e-01 bond pdb=" CA ASP Q 17 " pdb=" C ASP Q 17 " ideal model delta sigma weight residual 1.522 1.509 0.013 1.41e-02 5.03e+03 8.27e-01 bond pdb=" C ARG G 58 " pdb=" O ARG G 58 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 8.22e-01 ... (remaining 14439 not shown) Histogram of bond angle deviations from ideal: 102.33 - 108.65: 456 108.65 - 114.97: 8491 114.97 - 121.29: 7603 121.29 - 127.61: 3068 127.61 - 133.92: 47 Bond angle restraints: 19665 Sorted by residual: angle pdb=" N TYR C 8 " pdb=" CA TYR C 8 " pdb=" C TYR C 8 " ideal model delta sigma weight residual 111.14 114.14 -3.00 1.08e+00 8.57e-01 7.74e+00 angle pdb=" N TYR I 8 " pdb=" CA TYR I 8 " pdb=" C TYR I 8 " ideal model delta sigma weight residual 111.14 114.14 -3.00 1.08e+00 8.57e-01 7.73e+00 angle pdb=" N TYR R 8 " pdb=" CA TYR R 8 " pdb=" C TYR R 8 " ideal model delta sigma weight residual 111.14 114.14 -3.00 1.08e+00 8.57e-01 7.71e+00 angle pdb=" N TYR D 8 " pdb=" CA TYR D 8 " pdb=" C TYR D 8 " ideal model delta sigma weight residual 111.14 114.13 -2.99 1.08e+00 8.57e-01 7.67e+00 angle pdb=" N TYR A 8 " pdb=" CA TYR A 8 " pdb=" C TYR A 8 " ideal model delta sigma weight residual 111.14 114.12 -2.98 1.08e+00 8.57e-01 7.63e+00 ... (remaining 19660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 7802 14.38 - 28.76: 707 28.76 - 43.13: 162 43.13 - 57.51: 69 57.51 - 71.89: 23 Dihedral angle restraints: 8763 sinusoidal: 3335 harmonic: 5428 Sorted by residual: dihedral pdb=" CA VAL T 20 " pdb=" C VAL T 20 " pdb=" N ASP T 21 " pdb=" CA ASP T 21 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL Q 20 " pdb=" C VAL Q 20 " pdb=" N ASP Q 21 " pdb=" CA ASP Q 21 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL M 20 " pdb=" C VAL M 20 " pdb=" N ASP M 21 " pdb=" CA ASP M 21 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 725 0.023 - 0.045: 741 0.045 - 0.068: 518 0.068 - 0.090: 201 0.090 - 0.113: 69 Chirality restraints: 2254 Sorted by residual: chirality pdb=" CA VAL E 20 " pdb=" N VAL E 20 " pdb=" C VAL E 20 " pdb=" CB VAL E 20 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA VAL C 20 " pdb=" N VAL C 20 " pdb=" C VAL C 20 " pdb=" CB VAL C 20 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA VAL U 20 " pdb=" N VAL U 20 " pdb=" C VAL U 20 " pdb=" CB VAL U 20 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.08e-01 ... (remaining 2251 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 57 " -0.015 2.00e-02 2.50e+03 1.04e-02 2.16e+00 pdb=" CG TYR N 57 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR N 57 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR N 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR N 57 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR N 57 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR N 57 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR N 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 57 " -0.015 2.00e-02 2.50e+03 1.03e-02 2.14e+00 pdb=" CG TYR J 57 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR J 57 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR J 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR J 57 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 57 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR J 57 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR J 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 57 " -0.015 2.00e-02 2.50e+03 1.03e-02 2.12e+00 pdb=" CG TYR Q 57 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 57 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 57 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 57 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR Q 57 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR Q 57 " -0.002 2.00e-02 2.50e+03 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 356 2.71 - 3.26: 14394 3.26 - 3.80: 21903 3.80 - 4.35: 25819 4.35 - 4.90: 46098 Nonbonded interactions: 108570 Sorted by model distance: nonbonded pdb=" OD1 ASP E 10 " pdb=" OG SER K 49 " model vdw 2.160 2.440 nonbonded pdb=" OD2 ASP B 10 " pdb=" NZ LYS H 50 " model vdw 2.197 2.520 nonbonded pdb=" NZ LYS Q 50 " pdb=" OD2 ASP W 10 " model vdw 2.200 2.520 nonbonded pdb=" NZ LYS C 50 " pdb=" OD2 ASP P 10 " model vdw 2.209 2.520 nonbonded pdb=" OG SER F 49 " pdb=" OD1 ASP M 10 " model vdw 2.215 2.440 ... (remaining 108565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.010 Extract box with map and model: 6.280 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 39.280 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.140 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.006 0.026 14444 Z= 0.357 Angle : 0.836 4.325 19665 Z= 0.624 Chirality : 0.045 0.113 2254 Planarity : 0.004 0.031 2576 Dihedral : 13.444 71.891 5221 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.03 % Allowed : 7.18 % Favored : 89.79 % 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: 0.52 (0.18), residues: 1771 helix: 1.27 (0.12), residues: 1449 sheet: None (None), residues: 0 loop : -4.04 (0.23), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 5 PHE 0.006 0.001 PHE T 68 TYR 0.025 0.003 TYR N 57 ARG 0.001 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 1.454 Fit side-chains REVERT: A 53 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 57 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8041 (t80) REVERT: B 17 ASP cc_start: 0.7579 (m-30) cc_final: 0.7261 (m-30) REVERT: B 22 ASN cc_start: 0.7391 (t0) cc_final: 0.6967 (t0) REVERT: B 57 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8182 (t80) REVERT: C 17 ASP cc_start: 0.7380 (m-30) cc_final: 0.6861 (m-30) REVERT: C 57 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7699 (t80) REVERT: D 17 ASP cc_start: 0.7548 (m-30) cc_final: 0.7320 (m-30) REVERT: D 22 ASN cc_start: 0.7498 (t0) cc_final: 0.7292 (t0) REVERT: E 17 ASP cc_start: 0.7464 (m-30) cc_final: 0.7053 (m-30) REVERT: F 17 ASP cc_start: 0.7607 (m-30) cc_final: 0.7256 (m-30) REVERT: F 53 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7841 (mm-30) REVERT: F 57 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.8289 (t80) REVERT: L 18 THR cc_start: 0.8296 (m) cc_final: 0.8026 (p) REVERT: M 57 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7882 (t80) REVERT: N 53 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7749 (mm-30) REVERT: N 57 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7790 (t80) REVERT: O 17 ASP cc_start: 0.7738 (m-30) cc_final: 0.7389 (m-30) REVERT: O 53 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7680 (mm-30) REVERT: O 57 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8172 (t80) REVERT: P 53 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7388 (mm-30) REVERT: P 57 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8272 (t80) REVERT: Q 53 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7554 (mm-30) REVERT: Q 57 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7655 (t80) REVERT: R 17 ASP cc_start: 0.7659 (m-30) cc_final: 0.7426 (m-30) REVERT: R 53 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7227 (mm-30) REVERT: R 57 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8346 (t80) REVERT: S 57 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8347 (t80) REVERT: T 57 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8398 (t80) REVERT: U 70 ASP cc_start: 0.7785 (m-30) cc_final: 0.7540 (m-30) outliers start: 46 outliers final: 10 residues processed: 272 average time/residue: 0.2370 time to fit residues: 95.8582 Evaluate side-chains 241 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 219 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain W residue 57 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 126 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 14444 Z= 0.140 Angle : 0.400 3.012 19665 Z= 0.225 Chirality : 0.034 0.128 2254 Planarity : 0.004 0.032 2576 Dihedral : 7.590 59.566 1999 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.31 % Allowed : 11.07 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.19), residues: 1771 helix: 2.97 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -2.41 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 5 PHE 0.005 0.001 PHE F 68 TYR 0.012 0.002 TYR P 57 ARG 0.001 0.000 ARG T 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 1.614 Fit side-chains REVERT: A 17 ASP cc_start: 0.7465 (m-30) cc_final: 0.7085 (m-30) REVERT: A 57 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 17 ASP cc_start: 0.7316 (m-30) cc_final: 0.7025 (m-30) REVERT: C 17 ASP cc_start: 0.7250 (m-30) cc_final: 0.6880 (m-30) REVERT: C 57 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7876 (t80) REVERT: E 17 ASP cc_start: 0.7041 (m-30) cc_final: 0.6831 (m-30) REVERT: F 53 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7747 (mm-30) REVERT: J 6 SER cc_start: 0.9090 (p) cc_final: 0.8786 (p) REVERT: J 53 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7451 (mm-30) REVERT: K 53 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7275 (mm-30) REVERT: M 57 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7768 (t80) REVERT: M 69 LYS cc_start: 0.7932 (tmtt) cc_final: 0.7593 (tttm) REVERT: N 17 ASP cc_start: 0.7220 (m-30) cc_final: 0.6452 (m-30) REVERT: N 57 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7742 (t80) REVERT: O 57 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7826 (t80) REVERT: P 53 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7374 (mm-30) REVERT: P 57 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.8032 (t80) REVERT: Q 53 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7410 (mm-30) REVERT: Q 57 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7474 (t80) REVERT: R 53 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7171 (mm-30) REVERT: S 17 ASP cc_start: 0.7511 (m-30) cc_final: 0.7200 (m-30) REVERT: T 57 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7932 (t80) REVERT: T 72 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7641 (t0) REVERT: U 53 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7259 (mm-30) REVERT: V 53 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7257 (mm-30) outliers start: 35 outliers final: 18 residues processed: 259 average time/residue: 0.2752 time to fit residues: 102.5141 Evaluate side-chains 241 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 70 ASP Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain W residue 57 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 14444 Z= 0.144 Angle : 0.371 2.953 19665 Z= 0.206 Chirality : 0.034 0.119 2254 Planarity : 0.004 0.035 2576 Dihedral : 6.939 64.928 1993 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.04 % Allowed : 14.43 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.20), residues: 1771 helix: 3.52 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.57 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP U 5 PHE 0.006 0.001 PHE L 68 TYR 0.015 0.002 TYR S 57 ARG 0.001 0.000 ARG U 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 1.606 Fit side-chains REVERT: A 17 ASP cc_start: 0.7397 (m-30) cc_final: 0.7058 (m-30) REVERT: A 57 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7895 (t80) REVERT: C 57 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7780 (t80) REVERT: E 17 ASP cc_start: 0.7217 (m-30) cc_final: 0.7009 (m-30) REVERT: E 53 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7079 (mm-30) REVERT: F 53 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7511 (mm-30) REVERT: H 69 LYS cc_start: 0.8321 (tmtt) cc_final: 0.7888 (tttp) REVERT: J 6 SER cc_start: 0.9059 (p) cc_final: 0.8798 (p) REVERT: J 53 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7392 (mm-30) REVERT: J 69 LYS cc_start: 0.8231 (tmtt) cc_final: 0.8017 (tmtt) REVERT: L 53 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7190 (mm-30) REVERT: M 57 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7827 (t80) REVERT: M 69 LYS cc_start: 0.7896 (tmtt) cc_final: 0.7497 (tttm) REVERT: N 57 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7851 (t80) REVERT: P 53 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7309 (mm-30) REVERT: P 57 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8037 (t80) REVERT: Q 53 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7290 (mm-30) REVERT: Q 57 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7564 (t80) REVERT: R 53 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7023 (mm-30) REVERT: S 53 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7285 (mm-30) REVERT: T 17 ASP cc_start: 0.7497 (m-30) cc_final: 0.7101 (m-30) REVERT: T 57 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7730 (t80) REVERT: V 53 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7103 (mm-30) outliers start: 31 outliers final: 17 residues processed: 234 average time/residue: 0.2464 time to fit residues: 85.3491 Evaluate side-chains 233 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain W residue 57 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN U 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 14444 Z= 0.128 Angle : 0.346 2.774 19665 Z= 0.191 Chirality : 0.033 0.120 2254 Planarity : 0.004 0.037 2576 Dihedral : 6.341 64.674 1989 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.98 % Allowed : 15.15 % Favored : 82.87 % 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: 4.52 (0.20), residues: 1771 helix: 3.75 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.52 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP U 5 PHE 0.004 0.001 PHE L 68 TYR 0.013 0.001 TYR B 57 ARG 0.000 0.000 ARG T 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 1.624 Fit side-chains REVERT: C 57 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7826 (t80) REVERT: F 53 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7743 (mm-30) REVERT: H 69 LYS cc_start: 0.8129 (tmtt) cc_final: 0.7656 (tttp) REVERT: J 53 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7428 (mm-30) REVERT: L 53 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7282 (mm-30) REVERT: M 57 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7767 (t80) REVERT: M 69 LYS cc_start: 0.7859 (tmtt) cc_final: 0.7447 (tttm) REVERT: N 17 ASP cc_start: 0.7007 (m-30) cc_final: 0.6413 (m-30) REVERT: N 57 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7815 (t80) REVERT: O 57 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7837 (t80) REVERT: P 53 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7298 (mm-30) REVERT: Q 53 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7326 (mm-30) REVERT: Q 57 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7594 (t80) REVERT: R 53 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6974 (mm-30) REVERT: S 53 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7223 (mm-30) REVERT: T 17 ASP cc_start: 0.7295 (m-30) cc_final: 0.6830 (m-30) REVERT: T 57 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7633 (t80) REVERT: T 72 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7518 (t0) REVERT: V 53 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7182 (mm-30) outliers start: 30 outliers final: 16 residues processed: 249 average time/residue: 0.2583 time to fit residues: 92.7075 Evaluate side-chains 238 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain W residue 57 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN E 24 GLN U 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 14444 Z= 0.138 Angle : 0.350 2.840 19665 Z= 0.192 Chirality : 0.033 0.118 2254 Planarity : 0.004 0.034 2576 Dihedral : 6.083 68.853 1981 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.52 % Allowed : 16.14 % Favored : 82.35 % 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: 4.66 (0.20), residues: 1771 helix: 3.83 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.38 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 5 PHE 0.005 0.001 PHE Q 68 TYR 0.014 0.002 TYR R 57 ARG 0.001 0.000 ARG U 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 1.573 Fit side-chains REVERT: H 69 LYS cc_start: 0.8116 (tmtt) cc_final: 0.7644 (tttp) REVERT: J 53 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7378 (mm-30) REVERT: M 57 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7823 (t80) REVERT: M 69 LYS cc_start: 0.7928 (tmtt) cc_final: 0.7513 (tttm) REVERT: O 57 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7878 (t80) REVERT: P 53 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7296 (mm-30) REVERT: P 57 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.8104 (t80) REVERT: Q 53 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7311 (mm-30) REVERT: Q 57 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7496 (t80) REVERT: R 53 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6959 (mm-30) REVERT: S 53 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7208 (mm-30) REVERT: T 17 ASP cc_start: 0.7261 (m-30) cc_final: 0.6826 (m-30) REVERT: T 57 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7642 (t80) REVERT: V 53 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7096 (mm-30) outliers start: 23 outliers final: 12 residues processed: 234 average time/residue: 0.2418 time to fit residues: 84.1327 Evaluate side-chains 231 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 214 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN U 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 14444 Z= 0.309 Angle : 0.470 4.342 19665 Z= 0.257 Chirality : 0.038 0.121 2254 Planarity : 0.004 0.032 2576 Dihedral : 6.379 72.318 1973 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.91 % Allowed : 16.67 % Favored : 81.42 % 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: 4.29 (0.20), residues: 1771 helix: 3.61 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.66 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 5 PHE 0.008 0.002 PHE T 68 TYR 0.026 0.003 TYR E 57 ARG 0.002 0.000 ARG Q 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 1.687 Fit side-chains REVERT: C 57 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7776 (t80) REVERT: D 57 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7912 (t80) REVERT: J 53 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7285 (mm-30) REVERT: M 57 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7927 (t80) REVERT: N 57 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7808 (t80) REVERT: P 53 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7506 (mm-30) REVERT: P 57 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8239 (t80) REVERT: Q 53 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7280 (mm-30) REVERT: Q 57 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7726 (t80) REVERT: R 53 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6971 (mm-30) REVERT: S 53 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7190 (mm-30) REVERT: T 53 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7253 (mm-30) REVERT: T 57 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7843 (t80) REVERT: T 72 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8006 (t0) REVERT: U 5 TRP cc_start: 0.8604 (t60) cc_final: 0.8275 (t60) REVERT: V 53 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7063 (mm-30) REVERT: V 72 ASP cc_start: 0.8032 (m-30) cc_final: 0.7762 (m-30) outliers start: 29 outliers final: 17 residues processed: 241 average time/residue: 0.2192 time to fit residues: 80.9666 Evaluate side-chains 243 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 94 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN O 63 ASN U 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14444 Z= 0.126 Angle : 0.343 2.725 19665 Z= 0.190 Chirality : 0.033 0.121 2254 Planarity : 0.004 0.033 2576 Dihedral : 5.829 68.381 1973 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.71 % Allowed : 18.05 % Favored : 80.24 % 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: 4.57 (0.20), residues: 1771 helix: 3.79 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP U 5 PHE 0.005 0.001 PHE L 68 TYR 0.012 0.001 TYR B 57 ARG 0.001 0.000 ARG T 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 1.593 Fit side-chains REVERT: C 17 ASP cc_start: 0.7196 (m-30) cc_final: 0.6818 (m-30) REVERT: C 57 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7832 (t80) REVERT: H 69 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7591 (tttp) REVERT: M 57 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7766 (t80) REVERT: M 69 LYS cc_start: 0.7921 (tmtt) cc_final: 0.7524 (tttm) REVERT: N 17 ASP cc_start: 0.6822 (m-30) cc_final: 0.6244 (m-30) REVERT: N 57 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7751 (t80) REVERT: O 17 ASP cc_start: 0.7387 (m-30) cc_final: 0.6971 (m-30) REVERT: O 57 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7901 (t80) REVERT: P 17 ASP cc_start: 0.6941 (m-30) cc_final: 0.6545 (m-30) REVERT: P 53 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7302 (mm-30) REVERT: P 57 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8029 (t80) REVERT: Q 53 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7321 (mm-30) REVERT: Q 57 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7476 (t80) REVERT: R 53 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6963 (mm-30) REVERT: S 53 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7192 (mm-30) REVERT: T 57 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7638 (t80) REVERT: U 5 TRP cc_start: 0.8455 (t60) cc_final: 0.8203 (t60) REVERT: V 53 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7022 (mm-30) outliers start: 26 outliers final: 11 residues processed: 234 average time/residue: 0.2449 time to fit residues: 84.8703 Evaluate side-chains 232 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN E 24 GLN O 63 ASN U 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 14444 Z= 0.161 Angle : 0.368 3.159 19665 Z= 0.202 Chirality : 0.034 0.120 2254 Planarity : 0.004 0.036 2576 Dihedral : 5.774 69.400 1973 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.12 % Allowed : 18.84 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.58 (0.20), residues: 1771 helix: 3.80 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.50 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 5 PHE 0.005 0.001 PHE F 68 TYR 0.018 0.002 TYR A 57 ARG 0.001 0.000 ARG M 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 211 time to evaluate : 1.474 Fit side-chains REVERT: C 57 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7835 (t80) REVERT: F 53 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7682 (mm-30) REVERT: H 69 LYS cc_start: 0.8136 (tmtt) cc_final: 0.7665 (tttp) REVERT: M 57 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7828 (t80) REVERT: M 69 LYS cc_start: 0.7980 (tmtt) cc_final: 0.7592 (tttm) REVERT: N 57 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7741 (t80) REVERT: P 53 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7385 (mm-30) REVERT: P 57 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8157 (t80) REVERT: Q 53 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7251 (mm-30) REVERT: Q 57 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7584 (t80) REVERT: R 53 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6873 (mm-30) REVERT: S 53 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7198 (mm-30) REVERT: T 53 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7204 (mm-30) REVERT: T 57 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7676 (t80) REVERT: U 5 TRP cc_start: 0.8473 (t60) cc_final: 0.8217 (t60) REVERT: V 53 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6949 (mm-30) outliers start: 17 outliers final: 9 residues processed: 226 average time/residue: 0.2379 time to fit residues: 80.6867 Evaluate side-chains 224 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 87 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 152 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN E 24 GLN O 63 ASN U 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14444 Z= 0.111 Angle : 0.325 2.773 19665 Z= 0.178 Chirality : 0.033 0.120 2254 Planarity : 0.004 0.034 2576 Dihedral : 5.320 65.294 1973 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.92 % Allowed : 18.91 % Favored : 80.17 % 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: 4.77 (0.20), residues: 1771 helix: 3.91 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 5 PHE 0.004 0.001 PHE L 68 TYR 0.011 0.001 TYR B 57 ARG 0.000 0.000 ARG T 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 226 time to evaluate : 1.536 Fit side-chains REVERT: C 17 ASP cc_start: 0.7230 (m-30) cc_final: 0.6991 (m-30) REVERT: C 57 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7898 (t80) REVERT: F 53 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7542 (mm-30) REVERT: G 53 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7230 (mm-30) REVERT: M 57 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7701 (t80) REVERT: O 17 ASP cc_start: 0.7420 (m-30) cc_final: 0.7032 (m-30) REVERT: O 57 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7869 (t80) REVERT: P 17 ASP cc_start: 0.6871 (m-30) cc_final: 0.6533 (m-30) REVERT: P 53 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7298 (mm-30) REVERT: P 57 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7982 (t80) REVERT: Q 53 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7331 (mm-30) REVERT: Q 57 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7420 (t80) REVERT: R 53 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6937 (mm-30) REVERT: S 53 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7173 (mm-30) REVERT: T 53 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7203 (mm-30) REVERT: T 57 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7608 (t80) REVERT: U 5 TRP cc_start: 0.8420 (t60) cc_final: 0.8156 (t60) REVERT: V 53 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6993 (mm-30) outliers start: 14 outliers final: 6 residues processed: 238 average time/residue: 0.2539 time to fit residues: 88.2285 Evaluate side-chains 229 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 217 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 chunk 78 optimal weight: 6.9990 chunk 101 optimal weight: 0.0980 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 63 ASN O 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14444 Z= 0.109 Angle : 0.325 4.880 19665 Z= 0.176 Chirality : 0.032 0.121 2254 Planarity : 0.004 0.037 2576 Dihedral : 4.793 61.835 1969 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.59 % Allowed : 19.63 % Favored : 79.78 % 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: 4.86 (0.20), residues: 1771 helix: 3.96 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.20 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 5 PHE 0.003 0.000 PHE L 68 TYR 0.012 0.001 TYR B 57 ARG 0.000 0.000 ARG U 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 1.519 Fit side-chains REVERT: F 53 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7475 (mm-30) REVERT: G 53 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7269 (mm-30) REVERT: H 69 LYS cc_start: 0.7812 (tmtt) cc_final: 0.7431 (tmtt) REVERT: P 53 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7305 (mm-30) REVERT: Q 53 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7378 (mm-30) REVERT: R 53 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6895 (mm-30) REVERT: S 53 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7156 (mm-30) REVERT: T 53 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7198 (mm-30) REVERT: T 57 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7571 (t80) REVERT: V 53 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7136 (mm-30) outliers start: 9 outliers final: 5 residues processed: 223 average time/residue: 0.2599 time to fit residues: 86.6557 Evaluate side-chains 219 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN E 24 GLN I 24 GLN N 24 GLN O 63 ASN P 63 ASN U 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110928 restraints weight = 15726.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114740 restraints weight = 9589.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117350 restraints weight = 6822.582| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14444 Z= 0.140 Angle : 0.353 4.571 19665 Z= 0.193 Chirality : 0.034 0.123 2254 Planarity : 0.004 0.038 2576 Dihedral : 4.387 63.616 1959 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.66 % Allowed : 19.89 % Favored : 79.45 % 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: 4.88 (0.20), residues: 1771 helix: 3.95 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.11 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 5 PHE 0.004 0.001 PHE L 68 TYR 0.015 0.002 TYR A 57 ARG 0.001 0.000 ARG P 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.21 seconds wall clock time: 47 minutes 22.99 seconds (2842.99 seconds total)