Starting phenix.real_space_refine on Sun Mar 17 17:20:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/03_2024/7z1t_14452.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/03_2024/7z1t_14452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/03_2024/7z1t_14452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/03_2024/7z1t_14452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/03_2024/7z1t_14452.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1t_14452/03_2024/7z1t_14452.pdb" } resolution = 2.26 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= 0.001 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 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.34, per 1000 atoms: 0.51 Number of scatterers: 18492 At special positions: 0 Unit cell: (100.062, 98.754, 158.922, 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: 6.87 Conformation dependent library (CDL) restraints added in 3.2 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: 72 helices and 12 sheets defined 75.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 177 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 177 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 177 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 177 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.391A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 177 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 177 Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU G 42 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 177 Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU H 42 " --> pdb=" O GLY H 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 177 Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER I 43 " --> pdb=" O THR I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 177 Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 3 through 16 removed outlier: 4.090A pdb=" N LEU J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU J 42 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER J 43 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 177 Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU K 7 " --> pdb=" O ASP K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU K 42 " --> pdb=" O GLY K 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER K 43 " --> pdb=" O THR K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 177 Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 3 through 16 removed outlier: 4.089A pdb=" N LEU L 7 " --> pdb=" O ASP L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 45 removed outlier: 4.390A pdb=" N VAL L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU L 42 " --> pdb=" O GLY L 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER L 43 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 177 Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 1416 hydrogen bonds defined for protein. 4176 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: 5.25 Time building geometry restraints manager: 7.49 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: 5391 1.34 - 1.46: 4689 1.46 - 1.58: 8808 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" C ASP G 190 " pdb=" N PRO G 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C ASP A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C ASP E 190 " pdb=" N PRO E 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 bond pdb=" C ASP K 190 " pdb=" N PRO K 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 bond pdb=" C ASP B 190 " pdb=" N PRO B 191 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.69e+00 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.59: 228 105.59 - 112.69: 10196 112.69 - 119.79: 5618 119.79 - 126.89: 9493 126.89 - 133.99: 265 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL I 87 " pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL L 87 " pdb=" CA VAL L 87 " pdb=" CB VAL L 87 " ideal model delta sigma weight residual 113.70 110.61 3.09 9.50e-01 1.11e+00 1.05e+01 angle pdb=" C VAL B 87 " pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta sigma weight residual 113.70 110.62 3.08 9.50e-01 1.11e+00 1.05e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 9828 17.21 - 34.42: 973 34.42 - 51.63: 227 51.63 - 68.83: 12 68.83 - 86.04: 24 Dihedral angle restraints: 11064 sinusoidal: 4392 harmonic: 6672 Sorted by residual: dihedral pdb=" CA TYR E 177 " pdb=" C TYR E 177 " pdb=" N GLY E 178 " pdb=" CA GLY E 178 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TYR D 177 " pdb=" C TYR D 177 " pdb=" N GLY D 178 " pdb=" CA GLY D 178 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N GLY A 178 " pdb=" CA GLY A 178 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1976 0.027 - 0.054: 598 0.054 - 0.080: 275 0.080 - 0.107: 79 0.107 - 0.134: 24 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA ARG D 202 " pdb=" N ARG D 202 " pdb=" C ARG D 202 " pdb=" CB ARG D 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ARG H 202 " pdb=" N ARG H 202 " pdb=" C ARG H 202 " pdb=" CB ARG H 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ARG J 202 " pdb=" N ARG J 202 " pdb=" C ARG J 202 " pdb=" CB ARG J 202 " both_signs ideal model delta sigma weight residual False 2.51 2.38 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=" CG GLU K 205 " 0.004 2.00e-02 2.50e+03 9.14e-03 8.36e-01 pdb=" CD GLU K 205 " -0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU K 205 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU K 205 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 205 " -0.004 2.00e-02 2.50e+03 9.12e-03 8.31e-01 pdb=" CD GLU H 205 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU H 205 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU H 205 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 205 " -0.004 2.00e-02 2.50e+03 9.06e-03 8.20e-01 pdb=" CD GLU B 205 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLU B 205 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU B 205 " -0.006 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 238 2.71 - 3.26: 18591 3.26 - 3.81: 32196 3.81 - 4.35: 36542 4.35 - 4.90: 62100 Nonbonded interactions: 149667 Sorted by model distance: nonbonded pdb=" O ILE L 72 " pdb=" OH TYR L 177 " model vdw 2.163 2.440 nonbonded pdb=" O ILE I 72 " pdb=" OH TYR I 177 " model vdw 2.163 2.440 nonbonded pdb=" O ILE F 72 " pdb=" OH TYR F 177 " model vdw 2.163 2.440 nonbonded pdb=" O ILE C 72 " pdb=" OH TYR C 177 " model vdw 2.163 2.440 nonbonded pdb=" O ILE J 72 " pdb=" OH TYR J 177 " model vdw 2.164 2.440 ... (remaining 149662 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: 3.320 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: 12.530 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 46.310 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 0.025 19008 Z= 0.174 Angle : 0.552 5.799 25800 Z= 0.307 Chirality : 0.034 0.134 2952 Planarity : 0.003 0.019 3096 Dihedral : 15.039 86.044 6636 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.17), residues: 2220 helix: 3.20 (0.11), residues: 1680 sheet: -0.64 (0.35), residues: 204 loop : -2.06 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 78 HIS 0.002 0.000 HIS G 74 PHE 0.012 0.001 PHE K 32 TYR 0.010 0.002 TYR A 66 ARG 0.003 0.000 ARG K 53 *********************** 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 372 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.049 Fit side-chains outliers start: 0 outliers final: 6 residues processed: 372 average time/residue: 1.3056 time to fit residues: 540.7694 Evaluate side-chains 329 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 323 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain L residue 12 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8375 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 19008 Z= 0.298 Angle : 0.550 6.235 25800 Z= 0.285 Chirality : 0.038 0.122 2952 Planarity : 0.003 0.023 3096 Dihedral : 4.038 38.226 2448 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.90 % Allowed : 14.31 % Favored : 80.78 % 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: 3.30 (0.17), residues: 2220 helix: 3.20 (0.11), residues: 1692 sheet: -0.24 (0.38), residues: 204 loop : -2.19 (0.25), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 4 HIS 0.001 0.001 HIS H 194 PHE 0.015 0.002 PHE F 32 TYR 0.020 0.002 TYR B 98 ARG 0.003 0.001 ARG B 76 *********************** 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 394 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 294 time to evaluate : 2.291 Fit side-chains REVERT: A 4 TRP cc_start: 0.7137 (OUTLIER) cc_final: 0.5332 (t-100) REVERT: A 202 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7871 (ptp-170) REVERT: B 202 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8019 (ptp-170) REVERT: C 202 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7941 (ptp-170) REVERT: D 4 TRP cc_start: 0.7132 (OUTLIER) cc_final: 0.5326 (t-100) REVERT: D 202 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7876 (ptp-170) REVERT: E 202 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8027 (ptp-170) REVERT: F 4 TRP cc_start: 0.7136 (OUTLIER) cc_final: 0.6014 (t-100) REVERT: F 202 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7936 (ptp-170) REVERT: G 4 TRP cc_start: 0.7135 (OUTLIER) cc_final: 0.5328 (t-100) REVERT: G 202 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7869 (ptp-170) REVERT: H 202 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8029 (ptp-170) REVERT: I 202 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7940 (ptp-170) REVERT: J 4 TRP cc_start: 0.7133 (OUTLIER) cc_final: 0.5326 (t-100) REVERT: J 202 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7863 (ptp-170) REVERT: K 202 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8026 (ptp-170) REVERT: L 202 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7934 (ptp-170) outliers start: 100 outliers final: 48 residues processed: 387 average time/residue: 1.3383 time to fit residues: 577.5216 Evaluate side-chains 353 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 288 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TRP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 4 TRP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 4 TRP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 220 SER Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 4 TRP Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 202 ARG Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain L residue 231 VAL 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: 1.9990 chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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: 0.8361 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19008 Z= 0.202 Angle : 0.489 5.990 25800 Z= 0.248 Chirality : 0.035 0.112 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.399 17.589 2436 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.28 % Allowed : 15.78 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.17), residues: 2220 helix: 3.36 (0.11), residues: 1692 sheet: -0.41 (0.36), residues: 204 loop : -2.19 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 4 HIS 0.001 0.000 HIS H 74 PHE 0.013 0.001 PHE J 32 TYR 0.016 0.001 TYR B 98 ARG 0.002 0.000 ARG E 76 *********************** 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 393 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 326 time to evaluate : 2.129 Fit side-chains REVERT: B 202 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7917 (ptp-170) REVERT: C 202 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7840 (ptp-170) REVERT: E 202 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7927 (ptp-170) REVERT: F 202 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7840 (ptp-170) REVERT: H 202 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7932 (ptp-170) REVERT: I 202 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7845 (ptp-170) REVERT: K 202 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7925 (ptp-170) REVERT: L 202 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7843 (ptp-170) outliers start: 67 outliers final: 37 residues processed: 382 average time/residue: 1.3810 time to fit residues: 584.9915 Evaluate side-chains 353 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 308 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19008 Z= 0.266 Angle : 0.515 6.802 25800 Z= 0.263 Chirality : 0.036 0.119 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.489 18.109 2436 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.46 % Allowed : 14.61 % Favored : 80.93 % 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: 3.41 (0.17), residues: 2220 helix: 3.31 (0.11), residues: 1692 sheet: -0.47 (0.37), residues: 204 loop : -2.13 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 4 HIS 0.002 0.001 HIS B 74 PHE 0.022 0.002 PHE F 232 TYR 0.017 0.002 TYR K 98 ARG 0.004 0.001 ARG G 101 *********************** 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 404 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 313 time to evaluate : 2.144 Fit side-chains REVERT: A 7 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8866 (tp) REVERT: B 202 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7964 (ptp-170) REVERT: C 202 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7888 (ptp-170) REVERT: D 7 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8870 (tp) REVERT: E 202 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7976 (ptp-170) REVERT: F 13 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8844 (tptp) REVERT: F 202 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7889 (ptp-170) REVERT: G 7 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8866 (tp) REVERT: H 202 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7980 (ptp-170) REVERT: I 202 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7892 (ptp-170) REVERT: J 7 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8856 (tp) REVERT: K 202 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7974 (ptp-170) REVERT: L 202 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7889 (ptp-170) outliers start: 91 outliers final: 57 residues processed: 389 average time/residue: 1.3519 time to fit residues: 584.1342 Evaluate side-chains 379 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 309 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 220 SER Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 19008 Z= 0.363 Angle : 0.554 7.018 25800 Z= 0.283 Chirality : 0.039 0.132 2952 Planarity : 0.004 0.020 3096 Dihedral : 3.640 18.847 2436 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 5.00 % Allowed : 15.20 % Favored : 79.80 % 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: 3.29 (0.17), residues: 2220 helix: 3.21 (0.11), residues: 1692 sheet: -0.40 (0.37), residues: 204 loop : -2.19 (0.25), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 174 HIS 0.002 0.001 HIS I 74 PHE 0.021 0.002 PHE D 232 TYR 0.018 0.002 TYR K 98 ARG 0.004 0.001 ARG D 101 *********************** 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 396 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 294 time to evaluate : 2.257 Fit side-chains REVERT: A 7 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8929 (tp) REVERT: B 202 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7987 (ptp-170) REVERT: C 202 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7938 (ptp-170) REVERT: D 7 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8931 (tp) REVERT: E 202 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8000 (ptp-170) REVERT: F 13 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8793 (tptp) REVERT: F 202 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7935 (ptp-170) REVERT: G 7 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8931 (tp) REVERT: H 202 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7997 (ptp-170) REVERT: I 13 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8787 (tptp) REVERT: I 202 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7940 (ptp-170) REVERT: J 7 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8931 (tp) REVERT: K 202 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7998 (ptp-170) REVERT: L 13 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8798 (tptp) REVERT: L 202 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7940 (ptp-170) outliers start: 102 outliers final: 64 residues processed: 382 average time/residue: 1.3005 time to fit residues: 553.9915 Evaluate side-chains 370 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 291 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 220 SER Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 231 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 202 ARG Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 220 SER Chi-restraints excluded: chain L residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 GLN F 49 GLN H 49 GLN K 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2747 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= 0.181 Angle : 0.481 6.280 25800 Z= 0.242 Chirality : 0.034 0.112 2952 Planarity : 0.003 0.017 3096 Dihedral : 3.407 18.005 2436 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.63 % Allowed : 16.23 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.17), residues: 2220 helix: 3.41 (0.11), residues: 1692 sheet: -0.69 (0.36), residues: 204 loop : -2.26 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 174 HIS 0.001 0.000 HIS E 74 PHE 0.011 0.001 PHE G 32 TYR 0.016 0.001 TYR E 98 ARG 0.003 0.000 ARG L 101 *********************** 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 383 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 309 time to evaluate : 2.115 Fit side-chains REVERT: I 13 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8776 (tptp) outliers start: 74 outliers final: 45 residues processed: 365 average time/residue: 1.3515 time to fit residues: 549.0596 Evaluate side-chains 344 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 298 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 100 MET Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 119 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN C 49 GLN D 49 GLN G 49 GLN I 49 GLN J 49 GLN K 49 GLN L 49 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19008 Z= 0.142 Angle : 0.444 7.680 25800 Z= 0.222 Chirality : 0.033 0.103 2952 Planarity : 0.002 0.017 3096 Dihedral : 3.242 16.723 2436 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.16 % Allowed : 16.96 % Favored : 80.88 % 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: 3.59 (0.17), residues: 2220 helix: 3.50 (0.11), residues: 1692 sheet: -0.75 (0.36), residues: 204 loop : -2.18 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 174 HIS 0.001 0.000 HIS H 74 PHE 0.011 0.001 PHE D 32 TYR 0.012 0.001 TYR H 98 ARG 0.004 0.000 ARG I 101 *********************** 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 376 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 332 time to evaluate : 2.127 Fit side-chains REVERT: F 13 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8746 (tptp) REVERT: L 13 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8744 (tptp) outliers start: 44 outliers final: 32 residues processed: 360 average time/residue: 1.3049 time to fit residues: 524.8261 Evaluate side-chains 350 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 316 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 40 optimal weight: 0.0170 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN C 49 GLN D 49 GLN E 49 GLN G 49 GLN H 49 GLN J 49 GLN K 49 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19008 Z= 0.149 Angle : 0.448 6.066 25800 Z= 0.224 Chirality : 0.033 0.106 2952 Planarity : 0.002 0.018 3096 Dihedral : 3.182 16.363 2436 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.96 % Allowed : 16.72 % Favored : 81.32 % 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: 3.58 (0.17), residues: 2220 helix: 3.48 (0.11), residues: 1692 sheet: -0.65 (0.35), residues: 204 loop : -2.16 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 4 HIS 0.001 0.000 HIS H 74 PHE 0.011 0.001 PHE G 32 TYR 0.014 0.001 TYR E 98 ARG 0.004 0.000 ARG L 101 *********************** 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 372 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 332 time to evaluate : 2.070 Fit side-chains REVERT: F 13 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8743 (tptp) REVERT: I 13 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8777 (tptp) REVERT: L 13 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8735 (tptp) outliers start: 40 outliers final: 34 residues processed: 361 average time/residue: 1.2834 time to fit residues: 517.9522 Evaluate side-chains 361 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 324 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 6.9990 chunk 181 optimal weight: 0.0870 chunk 194 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 49 GLN F 49 GLN I 49 GLN K 49 GLN L 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 19008 Z= 0.246 Angle : 0.497 6.576 25800 Z= 0.253 Chirality : 0.035 0.118 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.416 18.291 2436 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.65 % Allowed : 16.13 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.17), residues: 2220 helix: 3.37 (0.11), residues: 1692 sheet: -0.68 (0.36), residues: 204 loop : -2.13 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 174 HIS 0.001 0.000 HIS H 95 PHE 0.013 0.002 PHE A 32 TYR 0.014 0.002 TYR H 98 ARG 0.004 0.001 ARG L 101 *********************** 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 388 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 334 time to evaluate : 1.900 Fit side-chains REVERT: F 13 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8746 (tptp) REVERT: I 13 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8783 (tptp) REVERT: L 13 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8749 (tptp) outliers start: 54 outliers final: 50 residues processed: 384 average time/residue: 1.2153 time to fit residues: 524.1363 Evaluate side-chains 367 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 314 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 220 SER Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 220 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 220 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 198 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN E 49 GLN F 49 GLN H 49 GLN I 49 GLN K 49 GLN L 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19008 Z= 0.182 Angle : 0.453 5.968 25800 Z= 0.229 Chirality : 0.034 0.110 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.301 17.527 2436 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.11 % Allowed : 15.64 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.17), residues: 2220 helix: 3.44 (0.11), residues: 1692 sheet: -0.68 (0.36), residues: 204 loop : -2.21 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 4 HIS 0.001 0.000 HIS B 74 PHE 0.012 0.001 PHE G 32 TYR 0.010 0.001 TYR H 98 ARG 0.004 0.001 ARG L 101 ********************** 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 376 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 333 time to evaluate : 2.138 Fit side-chains REVERT: F 13 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8744 (tptp) REVERT: I 13 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8784 (tptp) REVERT: L 13 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8749 (tptp) outliers start: 43 outliers final: 40 residues processed: 369 average time/residue: 1.3217 time to fit residues: 543.5538 Evaluate side-chains 369 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 326 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN E 49 GLN H 49 GLN K 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.099812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.070521 restraints weight = 28354.885| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.67 r_work: 0.2798 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19008 Z= 0.137 Angle : 0.439 5.542 25800 Z= 0.222 Chirality : 0.033 0.103 2952 Planarity : 0.002 0.018 3096 Dihedral : 3.182 16.436 2436 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.81 % Allowed : 16.42 % Favored : 81.76 % 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: 3.60 (0.17), residues: 2220 helix: 3.51 (0.11), residues: 1692 sheet: -0.67 (0.36), residues: 204 loop : -2.23 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 4 HIS 0.001 0.000 HIS K 74 PHE 0.011 0.001 PHE J 32 TYR 0.011 0.001 TYR H 98 ARG 0.004 0.000 ARG G 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8396.17 seconds wall clock time: 147 minutes 57.11 seconds (8877.11 seconds total)