Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 21:19:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/04_2023/7z22_14455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/04_2023/7z22_14455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/04_2023/7z22_14455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/04_2023/7z22_14455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/04_2023/7z22_14455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/04_2023/7z22_14455.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 96 5.16 5 C 12396 2.51 5 N 2892 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "G TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G ASP 67": "OD1" <-> "OD2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 47": "OD1" <-> "OD2" Residue "I ASP 67": "OD1" <-> "OD2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 205": "OE1" <-> "OE2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J ASP 67": "OD1" <-> "OD2" Residue "J TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "K TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K ASP 67": "OD1" <-> "OD2" Residue "K TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 47": "OD1" <-> "OD2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "H" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Time building chain proxies: 9.90, per 1000 atoms: 0.54 Number of scatterers: 18492 At special positions: 0 Unit cell: (101.37, 98.754, 157.614, 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 96 16.00 O 3108 8.00 N 2892 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.20 Conformation dependent library (CDL) restraints added in 2.4 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 77.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.896A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR A 177 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.896A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.543A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR D 177 " --> pdb=" O GLN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR E 177 " --> pdb=" O GLN E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR F 177 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR G 177 " --> pdb=" O GLN G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR H 177 " --> pdb=" O GLN H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR I 177 " --> pdb=" O GLN I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR J 177 " --> pdb=" O GLN J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU K 7 " --> pdb=" O ASP K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR K 177 " --> pdb=" O GLN K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU L 7 " --> pdb=" O ASP L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR L 177 " --> pdb=" O GLN L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1380 hydrogen bonds defined for protein. 4104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 7.62 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: 5401 1.34 - 1.46: 4232 1.46 - 1.58: 9255 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" CB THR L 186 " pdb=" CG2 THR L 186 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CB THR F 186 " pdb=" CG2 THR F 186 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CB THR C 186 " pdb=" CG2 THR C 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.81e-01 bond pdb=" CB THR I 186 " pdb=" CG2 THR I 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.81e-01 bond pdb=" CB THR J 186 " pdb=" CG2 THR J 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.78e-01 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.48: 545 107.48 - 114.12: 10871 114.12 - 120.76: 8844 120.76 - 127.41: 5315 127.41 - 134.05: 225 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C VAL J 87 " pdb=" CA VAL J 87 " pdb=" CB VAL J 87 " ideal model delta sigma weight residual 113.70 110.28 3.42 9.50e-01 1.11e+00 1.29e+01 angle pdb=" C VAL I 87 " pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL L 87 " pdb=" CA VAL L 87 " pdb=" CB VAL L 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.46: 9059 8.46 - 16.92: 1148 16.92 - 25.38: 389 25.38 - 33.84: 348 33.84 - 42.30: 120 Dihedral angle restraints: 11064 sinusoidal: 4392 harmonic: 6672 Sorted by residual: dihedral pdb=" CA GLN L 173 " pdb=" CB GLN L 173 " pdb=" CG GLN L 173 " pdb=" CD GLN L 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 dihedral pdb=" CA GLN I 173 " pdb=" CB GLN I 173 " pdb=" CG GLN I 173 " pdb=" CD GLN I 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 dihedral pdb=" CA GLN C 173 " pdb=" CB GLN C 173 " pdb=" CG GLN C 173 " pdb=" CD GLN C 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1895 0.027 - 0.055: 725 0.055 - 0.082: 187 0.082 - 0.109: 108 0.109 - 0.137: 37 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA PRO B 203 " pdb=" N PRO B 203 " pdb=" C PRO B 203 " pdb=" CB PRO B 203 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PRO E 203 " pdb=" N PRO E 203 " pdb=" C PRO E 203 " pdb=" CB PRO E 203 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PRO D 203 " pdb=" N PRO D 203 " pdb=" C PRO D 203 " pdb=" CB PRO D 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 76 " -0.082 9.50e-02 1.11e+02 3.68e-02 9.51e-01 pdb=" NE ARG H 76 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG H 76 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 76 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 76 " -0.081 9.50e-02 1.11e+02 3.65e-02 9.34e-01 pdb=" NE ARG D 76 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG D 76 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 76 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 76 " 0.081 9.50e-02 1.11e+02 3.65e-02 9.33e-01 pdb=" NE ARG J 76 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG J 76 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG J 76 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1161 2.74 - 3.28: 18793 3.28 - 3.82: 32371 3.82 - 4.36: 33981 4.36 - 4.90: 62159 Nonbonded interactions: 148465 Sorted by model distance: nonbonded pdb=" OD1 ASN G 63 " pdb=" NH1 ARG L 53 " model vdw 2.198 2.520 nonbonded pdb=" NH1 ARG E 53 " pdb=" OD1 ASN F 63 " model vdw 2.198 2.520 nonbonded pdb=" NH1 ARG G 53 " pdb=" OD1 ASN H 63 " model vdw 2.199 2.520 nonbonded pdb=" NH1 ARG D 53 " pdb=" OD1 ASN E 63 " model vdw 2.199 2.520 nonbonded pdb=" OD1 ASN A 63 " pdb=" NH1 ARG F 53 " model vdw 2.199 2.520 ... (remaining 148460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.500 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 46.030 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.120 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 19008 Z= 0.178 Angle : 0.514 4.809 25800 Z= 0.298 Chirality : 0.036 0.137 2952 Planarity : 0.004 0.037 3096 Dihedral : 11.338 42.299 6636 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.00 % 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: 2.55 (0.18), residues: 2220 helix: 3.02 (0.11), residues: 1632 sheet: -1.64 (0.35), residues: 204 loop : -2.64 (0.31), residues: 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 754 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 18 residues processed: 754 average time/residue: 1.0816 time to fit residues: 928.6012 Evaluate side-chains 333 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 315 time to evaluate : 2.134 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 2.9708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 196 optimal weight: 0.1980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.5930 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 19008 Z= 0.259 Angle : 0.858 11.632 25800 Z= 0.411 Chirality : 0.042 0.118 2952 Planarity : 0.004 0.021 3096 Dihedral : 3.856 14.781 2436 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 5.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2220 helix: 2.44 (0.11), residues: 1644 sheet: -1.14 (0.37), residues: 204 loop : -2.26 (0.31), residues: 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 387 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 13 residues processed: 454 average time/residue: 0.9431 time to fit residues: 497.8853 Evaluate side-chains 332 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 319 time to evaluate : 2.114 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 12 average time/residue: 0.3066 time to fit residues: 8.3770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 157 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 195 GLN C 195 GLN D 195 GLN E 195 GLN F 195 GLN G 195 GLN H 195 GLN I 195 GLN J 195 GLN K 195 GLN L 195 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 19008 Z= 0.312 Angle : 0.784 10.306 25800 Z= 0.387 Chirality : 0.044 0.141 2952 Planarity : 0.004 0.027 3096 Dihedral : 3.998 13.791 2436 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 5.00 % 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: 1.64 (0.17), residues: 2220 helix: 2.13 (0.11), residues: 1644 sheet: -0.90 (0.38), residues: 204 loop : -2.64 (0.34), residues: 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 321 time to evaluate : 1.910 Fit side-chains outliers start: 102 outliers final: 29 residues processed: 391 average time/residue: 0.9547 time to fit residues: 434.7302 Evaluate side-chains 267 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 238 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 17 residues processed: 12 average time/residue: 0.2938 time to fit residues: 7.9034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 173 GLN C 173 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN H 173 GLN I 173 GLN ** J 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 1.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 19008 Z= 0.303 Angle : 0.765 10.810 25800 Z= 0.383 Chirality : 0.042 0.319 2952 Planarity : 0.004 0.028 3096 Dihedral : 3.852 17.819 2436 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 7.11 % 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: 1.88 (0.17), residues: 2220 helix: 2.37 (0.11), residues: 1632 sheet: -0.75 (0.37), residues: 204 loop : -2.81 (0.32), residues: 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 377 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 38 residues processed: 471 average time/residue: 1.0581 time to fit residues: 571.0327 Evaluate side-chains 332 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 294 time to evaluate : 2.159 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 25 residues processed: 17 average time/residue: 0.2456 time to fit residues: 9.6183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN C 173 GLN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 173 GLN G 173 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN I 173 GLN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 173 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 1.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19008 Z= 0.191 Angle : 0.697 10.915 25800 Z= 0.339 Chirality : 0.037 0.136 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.829 20.908 2436 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 6.62 % 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: 2.36 (0.17), residues: 2220 helix: 2.73 (0.11), residues: 1644 sheet: -0.62 (0.38), residues: 204 loop : -2.87 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 307 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 65 residues processed: 399 average time/residue: 1.0974 time to fit residues: 500.9100 Evaluate side-chains 355 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 290 time to evaluate : 2.143 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 45 residues processed: 28 average time/residue: 0.3128 time to fit residues: 15.7617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 0.4980 chunk 173 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 1.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19008 Z= 0.169 Angle : 0.700 12.654 25800 Z= 0.330 Chirality : 0.037 0.185 2952 Planarity : 0.003 0.017 3096 Dihedral : 3.713 20.989 2436 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 5.98 % 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: 2.68 (0.18), residues: 2220 helix: 3.00 (0.11), residues: 1644 sheet: -0.67 (0.38), residues: 204 loop : -2.83 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 329 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 62 residues processed: 402 average time/residue: 1.0904 time to fit residues: 501.9342 Evaluate side-chains 359 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 297 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 39 residues processed: 28 average time/residue: 0.3401 time to fit residues: 17.0973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 0.0970 chunk 208 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 173 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN K 173 GLN ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 1.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19008 Z= 0.186 Angle : 0.711 13.720 25800 Z= 0.337 Chirality : 0.038 0.190 2952 Planarity : 0.003 0.026 3096 Dihedral : 3.746 21.776 2436 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 5.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.18), residues: 2220 helix: 3.10 (0.11), residues: 1644 sheet: -0.60 (0.37), residues: 204 loop : -2.90 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 378 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 58 residues processed: 451 average time/residue: 0.9455 time to fit residues: 497.6050 Evaluate side-chains 387 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 329 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 44 residues processed: 22 average time/residue: 0.3272 time to fit residues: 13.3078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 173 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 173 GLN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN H 173 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN K 173 GLN ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 1.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19008 Z= 0.178 Angle : 0.722 14.617 25800 Z= 0.342 Chirality : 0.038 0.228 2952 Planarity : 0.003 0.023 3096 Dihedral : 3.782 22.478 2436 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 4.66 % 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: 2.87 (0.18), residues: 2220 helix: 3.15 (0.11), residues: 1644 sheet: -0.54 (0.37), residues: 204 loop : -2.90 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 343 time to evaluate : 2.442 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 outliers start: 95 outliers final: 67 residues processed: 399 average time/residue: 1.0021 time to fit residues: 461.3926 Evaluate side-chains 386 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 319 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 49 residues processed: 26 average time/residue: 0.3066 time to fit residues: 14.5932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 59 optimal weight: 0.0570 chunk 175 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 173 GLN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 1.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 19008 Z= 0.222 Angle : 0.769 14.363 25800 Z= 0.373 Chirality : 0.040 0.230 2952 Planarity : 0.003 0.037 3096 Dihedral : 3.989 26.147 2436 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 4.75 % 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: 2.79 (0.18), residues: 2220 helix: 3.07 (0.12), residues: 1644 sheet: -0.34 (0.36), residues: 204 loop : -2.96 (0.31), residues: 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 325 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 52 residues processed: 391 average time/residue: 0.9360 time to fit residues: 426.0148 Evaluate side-chains 351 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 299 time to evaluate : 2.135 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 46 residues processed: 10 average time/residue: 0.2929 time to fit residues: 7.2845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN D 224 ASN E 173 GLN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 GLN ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 1.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 19008 Z= 0.235 Angle : 0.796 14.281 25800 Z= 0.383 Chirality : 0.041 0.240 2952 Planarity : 0.003 0.041 3096 Dihedral : 4.000 25.344 2436 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.18), residues: 2220 helix: 3.01 (0.12), residues: 1644 sheet: -0.26 (0.37), residues: 204 loop : -2.99 (0.31), residues: 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 321 time to evaluate : 2.172 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 41 residues processed: 366 average time/residue: 1.0972 time to fit residues: 461.6897 Evaluate side-chains 321 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 280 time to evaluate : 2.412 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 39 residues processed: 6 average time/residue: 0.4145 time to fit residues: 6.4975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 176 optimal weight: 0.0010 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 173 GLN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN D 224 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN F 15 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN G 224 ASN H 15 GLN H 173 GLN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN J 224 ASN K 15 GLN K 173 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.093446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072042 restraints weight = 48026.399| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.94 r_work: 0.3090 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 1.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19008 Z= 0.181 Angle : 0.741 13.860 25800 Z= 0.347 Chirality : 0.038 0.219 2952 Planarity : 0.003 0.022 3096 Dihedral : 3.795 22.347 2436 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 3.58 % 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: 2.88 (0.18), residues: 2220 helix: 3.15 (0.12), residues: 1644 sheet: -0.33 (0.37), residues: 204 loop : -2.97 (0.31), residues: 372 =============================================================================== Job complete usr+sys time: 7869.38 seconds wall clock time: 139 minutes 47.76 seconds (8387.76 seconds total)