Starting phenix.real_space_refine on Sun Mar 17 16:43:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/03_2024/7zxp_15013.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/03_2024/7zxp_15013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/03_2024/7zxp_15013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/03_2024/7zxp_15013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/03_2024/7zxp_15013.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxp_15013/03_2024/7zxp_15013.pdb" } resolution = 2.39 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= 0.002 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 168 5.16 5 C 12192 2.51 5 N 3060 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 46": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 46": "OD1" <-> "OD2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 46": "OD1" <-> "OD2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 46": "OD1" <-> "OD2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 46": "OD1" <-> "OD2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L PHE 141": "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: 18420 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "B" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "D" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "E" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "F" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "G" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "H" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "I" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "K" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "L" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1535 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Time building chain proxies: 9.32, per 1000 atoms: 0.51 Number of scatterers: 18420 At special positions: 0 Unit cell: (106.602, 98.754, 164.154, 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 168 16.00 O 3000 8.00 N 3060 7.00 C 12192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 168 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.3 seconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 74.9% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 107 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 220 Processing helix chain 'B' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 107 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 220 Processing helix chain 'C' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 107 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 220 Processing helix chain 'D' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 107 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 134 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 220 Processing helix chain 'E' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 107 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 220 Processing helix chain 'F' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 107 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 134 " --> pdb=" O THR F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 220 Processing helix chain 'G' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 107 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP G 133 " --> pdb=" O GLY G 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 134 " --> pdb=" O THR G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 220 Processing helix chain 'H' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 107 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP H 133 " --> pdb=" O GLY H 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 220 Processing helix chain 'I' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 107 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP I 133 " --> pdb=" O GLY I 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR I 134 " --> pdb=" O THR I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 220 Processing helix chain 'J' and resid 21 through 43 removed outlier: 3.735A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 107 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 123 through 157 removed outlier: 3.598A pdb=" N TRP J 133 " --> pdb=" O GLY J 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR J 134 " --> pdb=" O THR J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 220 Processing helix chain 'K' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER K 42 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 107 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP K 133 " --> pdb=" O GLY K 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR K 134 " --> pdb=" O THR K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 220 Processing helix chain 'L' and resid 21 through 43 removed outlier: 3.736A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER L 42 " --> pdb=" O VAL L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 107 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 123 through 157 removed outlier: 3.599A pdb=" N TRP L 133 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.841A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1452 hydrogen bonds defined for protein. 4320 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: 5.19 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5544 1.35 - 1.46: 4666 1.46 - 1.58: 8474 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 18924 Sorted by residual: bond pdb=" CA THR D 86 " pdb=" C THR D 86 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.26e-02 6.30e+03 9.91e-01 bond pdb=" CA THR G 86 " pdb=" C THR G 86 " ideal model delta sigma weight residual 1.522 1.534 -0.013 1.26e-02 6.30e+03 9.91e-01 bond pdb=" CA THR E 86 " pdb=" C THR E 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.82e-01 bond pdb=" CA THR K 86 " pdb=" C THR K 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.82e-01 bond pdb=" CA THR C 86 " pdb=" C THR C 86 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.58e-01 ... (remaining 18919 not shown) Histogram of bond angle deviations from ideal: 100.71 - 107.37: 686 107.37 - 114.03: 11036 114.03 - 120.69: 7791 120.69 - 127.35: 6009 127.35 - 134.01: 254 Bond angle restraints: 25776 Sorted by residual: angle pdb=" C THR K 86 " pdb=" N PRO K 87 " pdb=" CD PRO K 87 " ideal model delta sigma weight residual 125.00 130.76 -5.76 4.10e+00 5.95e-02 1.97e+00 angle pdb=" C THR I 86 " pdb=" N PRO I 87 " pdb=" CD PRO I 87 " ideal model delta sigma weight residual 125.00 130.75 -5.75 4.10e+00 5.95e-02 1.96e+00 angle pdb=" C THR L 86 " pdb=" N PRO L 87 " pdb=" CD PRO L 87 " ideal model delta sigma weight residual 125.00 130.75 -5.75 4.10e+00 5.95e-02 1.96e+00 angle pdb=" C THR H 86 " pdb=" N PRO H 87 " pdb=" CD PRO H 87 " ideal model delta sigma weight residual 125.00 130.72 -5.72 4.10e+00 5.95e-02 1.95e+00 angle pdb=" C THR B 86 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 125.00 130.71 -5.71 4.10e+00 5.95e-02 1.94e+00 ... (remaining 25771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.86: 9372 12.86 - 25.72: 1032 25.72 - 38.58: 420 38.58 - 51.44: 240 51.44 - 64.30: 36 Dihedral angle restraints: 11100 sinusoidal: 4320 harmonic: 6780 Sorted by residual: dihedral pdb=" CB CYS J 64 " pdb=" SG CYS J 64 " pdb=" SG CYS J 168 " pdb=" CB CYS J 168 " ideal model delta sinusoidal sigma weight residual -86.00 -117.20 31.20 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CB CYS D 64 " pdb=" SG CYS D 64 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual -86.00 -117.20 31.20 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual -86.00 -117.19 31.19 1 1.00e+01 1.00e-02 1.39e+01 ... (remaining 11097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2182 0.033 - 0.067: 590 0.067 - 0.100: 228 0.100 - 0.134: 12 0.134 - 0.167: 36 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CB VAL C 95 " pdb=" CA VAL C 95 " pdb=" CG1 VAL C 95 " pdb=" CG2 VAL C 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB VAL F 95 " pdb=" CA VAL F 95 " pdb=" CG1 VAL F 95 " pdb=" CG2 VAL F 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB VAL L 95 " pdb=" CA VAL L 95 " pdb=" CG1 VAL L 95 " pdb=" CG2 VAL L 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 3045 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.88e+00 pdb=" CG PHE H 29 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.87e+00 pdb=" CG PHE K 29 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE K 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE K 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE K 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE K 29 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE K 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 29 " -0.013 2.00e-02 2.50e+03 1.28e-02 2.86e+00 pdb=" CG PHE J 29 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE J 29 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE J 29 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE J 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE J 29 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE J 29 " 0.000 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 6007 2.85 - 3.36: 18839 3.36 - 3.87: 32223 3.87 - 4.39: 32415 4.39 - 4.90: 58673 Nonbonded interactions: 148157 Sorted by model distance: nonbonded pdb=" O LEU D 131 " pdb=" OG1 THR D 134 " model vdw 2.332 2.440 nonbonded pdb=" O LEU I 131 " pdb=" OG1 THR I 134 " model vdw 2.332 2.440 nonbonded pdb=" O LEU L 131 " pdb=" OG1 THR L 134 " model vdw 2.332 2.440 nonbonded pdb=" O LEU F 131 " pdb=" OG1 THR F 134 " model vdw 2.332 2.440 nonbonded pdb=" O LEU C 131 " pdb=" OG1 THR C 134 " model vdw 2.332 2.440 ... (remaining 148152 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: 2.310 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: 12.310 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 46.450 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.002 0.020 18924 Z= 0.128 Angle : 0.423 5.761 25776 Z= 0.242 Chirality : 0.039 0.167 3048 Planarity : 0.003 0.017 3084 Dihedral : 14.726 64.301 6576 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.17 % Allowed : 17.35 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.17), residues: 2244 helix: 4.00 (0.10), residues: 1632 sheet: -0.27 (0.43), residues: 204 loop : -1.17 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 132 HIS 0.003 0.001 HIS H 73 PHE 0.030 0.002 PHE H 29 TYR 0.008 0.001 TYR G 65 ARG 0.002 0.000 ARG I 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 290 time to evaluate : 2.092 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 314 average time/residue: 0.8361 time to fit residues: 308.6593 Evaluate side-chains 207 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 69 optimal weight: 0.0370 chunk 108 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 73 HIS D 73 HIS E 73 HIS F 73 HIS G 73 HIS H 73 HIS J 73 HIS K 73 HIS L 73 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 18924 Z= 0.247 Angle : 0.459 5.676 25776 Z= 0.247 Chirality : 0.040 0.169 3048 Planarity : 0.003 0.021 3084 Dihedral : 4.109 41.667 2504 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.65 % Allowed : 16.47 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.17), residues: 2244 helix: 4.13 (0.10), residues: 1632 sheet: -0.29 (0.42), residues: 204 loop : -0.82 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 133 HIS 0.006 0.001 HIS F 73 PHE 0.012 0.002 PHE K 68 TYR 0.014 0.001 TYR A 65 ARG 0.001 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 200 time to evaluate : 2.183 Fit side-chains REVERT: A 105 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2781 (tpp) REVERT: B 105 MET cc_start: 0.3130 (OUTLIER) cc_final: 0.2771 (tpt) REVERT: C 105 MET cc_start: 0.2914 (OUTLIER) cc_final: 0.2615 (tpp) REVERT: D 105 MET cc_start: 0.3104 (OUTLIER) cc_final: 0.2744 (tpp) REVERT: E 105 MET cc_start: 0.3145 (OUTLIER) cc_final: 0.2790 (tpt) REVERT: F 105 MET cc_start: 0.2949 (OUTLIER) cc_final: 0.2649 (tpp) REVERT: G 105 MET cc_start: 0.3146 (OUTLIER) cc_final: 0.2792 (tpp) REVERT: H 105 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2779 (tpt) REVERT: I 105 MET cc_start: 0.2923 (OUTLIER) cc_final: 0.2623 (tpp) REVERT: J 105 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2779 (tpp) REVERT: K 105 MET cc_start: 0.3143 (OUTLIER) cc_final: 0.2772 (tpt) REVERT: L 105 MET cc_start: 0.2924 (OUTLIER) cc_final: 0.2616 (tpp) outliers start: 75 outliers final: 8 residues processed: 251 average time/residue: 0.9929 time to fit residues: 287.5676 Evaluate side-chains 190 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 105 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.8437 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 18924 Z= 0.143 Angle : 0.403 5.598 25776 Z= 0.212 Chirality : 0.038 0.161 3048 Planarity : 0.002 0.016 3084 Dihedral : 3.718 40.865 2492 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.90 % Allowed : 17.06 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.17), residues: 2244 helix: 4.37 (0.10), residues: 1632 sheet: -0.17 (0.43), residues: 204 loop : -0.87 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 24 HIS 0.004 0.000 HIS I 73 PHE 0.008 0.002 PHE D 190 TYR 0.012 0.001 TYR H 65 ARG 0.001 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 174 time to evaluate : 1.777 Fit side-chains REVERT: A 105 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2719 (tpp) REVERT: C 105 MET cc_start: 0.2897 (OUTLIER) cc_final: 0.2548 (tpp) REVERT: D 105 MET cc_start: 0.3142 (OUTLIER) cc_final: 0.2723 (tpp) REVERT: F 105 MET cc_start: 0.2892 (OUTLIER) cc_final: 0.2585 (tpp) REVERT: G 105 MET cc_start: 0.3148 (OUTLIER) cc_final: 0.2731 (tpp) REVERT: I 105 MET cc_start: 0.2893 (OUTLIER) cc_final: 0.2584 (tpp) REVERT: J 105 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2715 (tpp) REVERT: L 105 MET cc_start: 0.2895 (OUTLIER) cc_final: 0.2558 (tpp) outliers start: 80 outliers final: 44 residues processed: 230 average time/residue: 0.8959 time to fit residues: 241.4673 Evaluate side-chains 224 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 97 HIS Chi-restraints excluded: chain K residue 146 GLU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 198 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 HIS I 73 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 18924 Z= 0.156 Angle : 0.413 6.430 25776 Z= 0.218 Chirality : 0.038 0.206 3048 Planarity : 0.002 0.014 3084 Dihedral : 3.755 41.238 2492 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 4.53 % Allowed : 16.81 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.70 (0.16), residues: 2244 helix: 4.35 (0.10), residues: 1632 sheet: -0.11 (0.43), residues: 204 loop : -0.87 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 133 HIS 0.004 0.000 HIS C 73 PHE 0.009 0.002 PHE I 68 TYR 0.012 0.001 TYR B 65 ARG 0.001 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 188 time to evaluate : 2.232 Fit side-chains REVERT: B 105 MET cc_start: 0.3135 (OUTLIER) cc_final: 0.2770 (tpp) REVERT: B 131 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7157 (tp) REVERT: E 105 MET cc_start: 0.3147 (OUTLIER) cc_final: 0.2774 (tpp) REVERT: E 131 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7162 (tp) REVERT: H 105 MET cc_start: 0.3136 (OUTLIER) cc_final: 0.2767 (tpp) REVERT: H 131 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7160 (tp) REVERT: K 105 MET cc_start: 0.3147 (OUTLIER) cc_final: 0.2774 (tpp) REVERT: K 131 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7151 (tp) outliers start: 93 outliers final: 52 residues processed: 239 average time/residue: 0.8288 time to fit residues: 234.2872 Evaluate side-chains 244 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 184 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 97 HIS Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 146 GLU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 198 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 18924 Z= 0.171 Angle : 0.419 6.583 25776 Z= 0.221 Chirality : 0.038 0.190 3048 Planarity : 0.002 0.014 3084 Dihedral : 3.761 41.362 2492 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.95 % Allowed : 17.74 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.16), residues: 2244 helix: 4.37 (0.10), residues: 1632 sheet: -0.05 (0.43), residues: 204 loop : -0.93 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 24 HIS 0.002 0.000 HIS I 73 PHE 0.010 0.002 PHE B 68 TYR 0.012 0.001 TYR B 65 ARG 0.001 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 191 time to evaluate : 2.143 Fit side-chains REVERT: B 105 MET cc_start: 0.3185 (OUTLIER) cc_final: 0.2671 (tpp) REVERT: C 105 MET cc_start: 0.3094 (OUTLIER) cc_final: 0.2616 (tpp) REVERT: E 105 MET cc_start: 0.3185 (OUTLIER) cc_final: 0.2670 (tpp) REVERT: F 105 MET cc_start: 0.3098 (OUTLIER) cc_final: 0.2619 (tpp) REVERT: H 105 MET cc_start: 0.3176 (OUTLIER) cc_final: 0.2655 (tpp) REVERT: I 105 MET cc_start: 0.3092 (OUTLIER) cc_final: 0.2620 (tpp) REVERT: K 105 MET cc_start: 0.3122 (OUTLIER) cc_final: 0.2617 (tpp) REVERT: L 105 MET cc_start: 0.3084 (OUTLIER) cc_final: 0.2607 (tpp) outliers start: 81 outliers final: 46 residues processed: 226 average time/residue: 0.9412 time to fit residues: 247.3261 Evaluate side-chains 242 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 146 GLU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 198 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.2980 chunk 198 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS D 97 HIS E 97 HIS G 97 HIS H 97 HIS J 97 HIS K 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 18924 Z= 0.156 Angle : 0.404 6.678 25776 Z= 0.213 Chirality : 0.038 0.190 3048 Planarity : 0.002 0.014 3084 Dihedral : 3.697 41.348 2492 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.14 % Allowed : 17.15 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.16), residues: 2244 helix: 4.45 (0.10), residues: 1632 sheet: -0.01 (0.44), residues: 204 loop : -0.96 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 24 HIS 0.002 0.000 HIS B 73 PHE 0.009 0.002 PHE G 180 TYR 0.012 0.001 TYR D 65 ARG 0.001 0.000 ARG J 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 191 time to evaluate : 2.336 Fit side-chains REVERT: A 105 MET cc_start: 0.3252 (OUTLIER) cc_final: 0.2875 (tpp) REVERT: D 105 MET cc_start: 0.3253 (OUTLIER) cc_final: 0.2875 (tpp) REVERT: G 105 MET cc_start: 0.3255 (OUTLIER) cc_final: 0.2881 (tpp) REVERT: J 105 MET cc_start: 0.3250 (OUTLIER) cc_final: 0.2884 (tpp) outliers start: 85 outliers final: 50 residues processed: 228 average time/residue: 0.9284 time to fit residues: 248.2432 Evaluate side-chains 242 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 105 MET Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 146 GLU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 40.0000 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 123 optimal weight: 30.0000 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 18924 Z= 0.244 Angle : 0.446 6.704 25776 Z= 0.237 Chirality : 0.040 0.191 3048 Planarity : 0.003 0.017 3084 Dihedral : 3.905 42.285 2492 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.75 % Allowed : 18.52 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.64 (0.16), residues: 2244 helix: 4.32 (0.10), residues: 1632 sheet: -0.15 (0.43), residues: 204 loop : -0.95 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 133 HIS 0.002 0.001 HIS I 73 PHE 0.013 0.002 PHE A 180 TYR 0.013 0.001 TYR E 65 ARG 0.001 0.000 ARG L 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 169 time to evaluate : 2.313 Fit side-chains outliers start: 77 outliers final: 44 residues processed: 221 average time/residue: 0.9984 time to fit residues: 254.8803 Evaluate side-chains 210 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 146 GLU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 18924 Z= 0.125 Angle : 0.384 6.646 25776 Z= 0.204 Chirality : 0.037 0.185 3048 Planarity : 0.002 0.013 3084 Dihedral : 3.614 40.732 2492 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.83 % Allowed : 19.01 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.94 (0.17), residues: 2244 helix: 4.56 (0.09), residues: 1632 sheet: -0.00 (0.44), residues: 204 loop : -1.01 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 132 HIS 0.001 0.000 HIS I 73 PHE 0.007 0.001 PHE G 180 TYR 0.011 0.001 TYR G 65 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 196 time to evaluate : 2.088 Fit side-chains outliers start: 58 outliers final: 40 residues processed: 224 average time/residue: 0.9294 time to fit residues: 243.3684 Evaluate side-chains 232 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 146 GLU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 146 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 40.0000 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 123 optimal weight: 40.0000 chunk 89 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 18924 Z= 0.259 Angle : 0.445 6.717 25776 Z= 0.239 Chirality : 0.040 0.190 3048 Planarity : 0.003 0.017 3084 Dihedral : 3.891 42.239 2492 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.36 % Allowed : 18.86 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.71 (0.16), residues: 2244 helix: 4.38 (0.09), residues: 1632 sheet: -0.20 (0.43), residues: 204 loop : -0.94 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 133 HIS 0.003 0.001 HIS C 73 PHE 0.013 0.002 PHE E 68 TYR 0.013 0.001 TYR J 65 ARG 0.001 0.000 ARG F 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 172 time to evaluate : 2.228 Fit side-chains outliers start: 69 outliers final: 46 residues processed: 219 average time/residue: 1.0518 time to fit residues: 265.1387 Evaluate side-chains 214 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 168 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 146 GLU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 146 GLU Chi-restraints excluded: chain L residue 198 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 180 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 18924 Z= 0.211 Angle : 0.425 6.695 25776 Z= 0.228 Chirality : 0.039 0.187 3048 Planarity : 0.002 0.016 3084 Dihedral : 3.813 41.787 2492 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.02 % Allowed : 19.40 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.16), residues: 2244 helix: 4.40 (0.09), residues: 1632 sheet: -0.19 (0.43), residues: 204 loop : -0.96 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 44 HIS 0.002 0.000 HIS I 73 PHE 0.012 0.002 PHE B 68 TYR 0.012 0.001 TYR E 65 ARG 0.001 0.000 ARG G 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 191 time to evaluate : 2.220 Fit side-chains REVERT: C 93 MET cc_start: 0.8064 (mtt) cc_final: 0.7833 (mtt) REVERT: I 93 MET cc_start: 0.8061 (mtt) cc_final: 0.7827 (mtt) REVERT: L 93 MET cc_start: 0.8057 (mtt) cc_final: 0.7822 (mtt) outliers start: 62 outliers final: 44 residues processed: 228 average time/residue: 1.0077 time to fit residues: 265.4993 Evaluate side-chains 231 residues out of total 2052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 146 GLU Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 146 GLU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 146 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 97 HIS C 97 HIS D 97 HIS E 97 HIS F 97 HIS G 97 HIS H 97 HIS I 97 HIS J 97 HIS K 97 HIS L 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.130282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.078504 restraints weight = 25524.308| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.89 r_work: 0.2821 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 18924 Z= 0.173 Angle : 0.412 6.703 25776 Z= 0.221 Chirality : 0.038 0.186 3048 Planarity : 0.002 0.015 3084 Dihedral : 3.718 41.467 2492 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.83 % Allowed : 19.79 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.16), residues: 2244 helix: 4.50 (0.09), residues: 1632 sheet: -0.12 (0.43), residues: 204 loop : -0.99 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 44 HIS 0.002 0.000 HIS I 73 PHE 0.010 0.002 PHE E 68 TYR 0.016 0.001 TYR E 211 ARG 0.001 0.000 ARG I 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6304.88 seconds wall clock time: 112 minutes 6.34 seconds (6726.34 seconds total)