Starting phenix.real_space_refine on Mon Mar 25 02:10:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytq_10921/03_2024/6ytq_10921.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytq_10921/03_2024/6ytq_10921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytq_10921/03_2024/6ytq_10921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytq_10921/03_2024/6ytq_10921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytq_10921/03_2024/6ytq_10921.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytq_10921/03_2024/6ytq_10921.pdb" } resolution = 4.02 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= 0.006 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 440 5.16 5 C 29480 2.51 5 N 7678 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H ARG 174": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H GLU 233": "OE1" <-> "OE2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 174": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I ARG 247": "NH1" <-> "NH2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "J GLU 233": "OE1" <-> "OE2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "K GLU 233": "OE1" <-> "OE2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ARG 164": "NH1" <-> "NH2" Residue "L ARG 174": "NH1" <-> "NH2" Residue "L ARG 182": "NH1" <-> "NH2" Residue "L GLU 233": "OE1" <-> "OE2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M ARG 174": "NH1" <-> "NH2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 233": "OE1" <-> "OE2" Residue "M ARG 247": "NH1" <-> "NH2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N ARG 164": "NH1" <-> "NH2" Residue "N ARG 174": "NH1" <-> "NH2" Residue "N ARG 182": "NH1" <-> "NH2" Residue "N GLU 233": "OE1" <-> "OE2" Residue "N ARG 247": "NH1" <-> "NH2" Residue "O GLU 155": "OE1" <-> "OE2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O ARG 174": "NH1" <-> "NH2" Residue "O ARG 182": "NH1" <-> "NH2" Residue "O GLU 233": "OE1" <-> "OE2" Residue "O ARG 247": "NH1" <-> "NH2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P ARG 164": "NH1" <-> "NH2" Residue "P ARG 174": "NH1" <-> "NH2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "P ARG 247": "NH1" <-> "NH2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "Q ARG 174": "NH1" <-> "NH2" Residue "Q ARG 182": "NH1" <-> "NH2" Residue "Q GLU 233": "OE1" <-> "OE2" Residue "Q ARG 247": "NH1" <-> "NH2" Residue "R GLU 155": "OE1" <-> "OE2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 174": "NH1" <-> "NH2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R GLU 233": "OE1" <-> "OE2" Residue "R ARG 247": "NH1" <-> "NH2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S ARG 174": "NH1" <-> "NH2" Residue "S ARG 182": "NH1" <-> "NH2" Residue "S GLU 233": "OE1" <-> "OE2" Residue "S ARG 247": "NH1" <-> "NH2" Residue "T GLU 155": "OE1" <-> "OE2" Residue "T ARG 164": "NH1" <-> "NH2" Residue "T ARG 174": "NH1" <-> "NH2" Residue "T ARG 182": "NH1" <-> "NH2" Residue "T GLU 233": "OE1" <-> "OE2" Residue "T ARG 247": "NH1" <-> "NH2" Residue "U GLU 155": "OE1" <-> "OE2" Residue "U ARG 164": "NH1" <-> "NH2" Residue "U ARG 174": "NH1" <-> "NH2" Residue "U ARG 182": "NH1" <-> "NH2" Residue "U GLU 233": "OE1" <-> "OE2" Residue "U ARG 247": "NH1" <-> "NH2" Residue "V GLU 155": "OE1" <-> "OE2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V ARG 174": "NH1" <-> "NH2" Residue "V ARG 182": "NH1" <-> "NH2" Residue "V GLU 233": "OE1" <-> "OE2" Residue "V ARG 247": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45782 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "C" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "E" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "F" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "G" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "H" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "I" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "J" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "K" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "M" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "O" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "P" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "Q" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "R" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "S" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "T" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "U" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "V" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Time building chain proxies: 22.98, per 1000 atoms: 0.50 Number of scatterers: 45782 At special positions: 0 Unit cell: (140.7, 140.7, 207.7, 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 440 16.00 O 8184 8.00 N 7678 7.00 C 29480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 162 " distance=2.03 Simple disulfide: pdb=" SG CYS N 41 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 162 " distance=2.03 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 131 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 162 " distance=2.03 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 162 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 41 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 162 " distance=2.03 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 131 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 162 " distance=2.03 Simple disulfide: pdb=" SG CYS S 41 " - pdb=" SG CYS S 131 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 162 " distance=2.03 Simple disulfide: pdb=" SG CYS T 41 " - pdb=" SG CYS T 131 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 162 " distance=2.03 Simple disulfide: pdb=" SG CYS U 41 " - pdb=" SG CYS U 131 " distance=2.03 Simple disulfide: pdb=" SG CYS U 43 " - pdb=" SG CYS U 162 " distance=2.03 Simple disulfide: pdb=" SG CYS V 41 " - pdb=" SG CYS V 131 " distance=2.03 Simple disulfide: pdb=" SG CYS V 43 " - pdb=" SG CYS V 162 " 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: 18.45 Conformation dependent library (CDL) restraints added in 8.2 seconds 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11176 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.573A pdb=" N ILE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.756A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.541A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE A 145 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 146 " --> pdb=" O PRO A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 167 through 210 Processing helix chain 'A' and resid 216 through 253 Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.757A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.539A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE B 145 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 146 " --> pdb=" O PRO B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 167 through 210 Processing helix chain 'B' and resid 216 through 253 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 15 through 38 removed outlier: 3.604A pdb=" N ILE C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.757A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 4.096A pdb=" N CYS C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE C 145 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 146 " --> pdb=" O PRO C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 167 through 210 Processing helix chain 'C' and resid 216 through 253 Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.757A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.689A pdb=" N PHE D 145 " --> pdb=" O TYR D 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP D 146 " --> pdb=" O PRO D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 149 through 159 Processing helix chain 'D' and resid 167 through 210 Processing helix chain 'D' and resid 216 through 253 Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.968A pdb=" N PHE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.757A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 4.097A pdb=" N CYS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.687A pdb=" N PHE E 145 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 146 " --> pdb=" O PRO E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 146' Processing helix chain 'E' and resid 149 through 159 Processing helix chain 'E' and resid 167 through 210 Processing helix chain 'E' and resid 216 through 253 Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.757A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 112 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 146 " --> pdb=" O PRO F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 146' Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 167 through 210 Processing helix chain 'F' and resid 216 through 253 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.968A pdb=" N PHE G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.756A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.539A pdb=" N LEU G 116 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE G 145 " --> pdb=" O TYR G 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP G 146 " --> pdb=" O PRO G 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 142 through 146' Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 167 through 210 Processing helix chain 'G' and resid 216 through 253 Processing helix chain 'G' and resid 270 through 276 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.968A pdb=" N PHE H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.756A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 112 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE H 145 " --> pdb=" O TYR H 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP H 146 " --> pdb=" O PRO H 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 142 through 146' Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 167 through 210 Processing helix chain 'H' and resid 216 through 253 Processing helix chain 'H' and resid 270 through 276 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.968A pdb=" N PHE I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.757A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 112 Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.539A pdb=" N LEU I 116 " --> pdb=" O VAL I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.687A pdb=" N PHE I 145 " --> pdb=" O TYR I 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 146 " --> pdb=" O PRO I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 146' Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 167 through 210 Processing helix chain 'I' and resid 216 through 253 Processing helix chain 'I' and resid 270 through 276 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 15 through 38 removed outlier: 3.604A pdb=" N ILE J 19 " --> pdb=" O ASN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.756A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 112 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.539A pdb=" N LEU J 116 " --> pdb=" O VAL J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE J 145 " --> pdb=" O TYR J 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP J 146 " --> pdb=" O PRO J 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 142 through 146' Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 167 through 210 Processing helix chain 'J' and resid 216 through 253 Processing helix chain 'J' and resid 270 through 276 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 15 through 38 removed outlier: 3.604A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.968A pdb=" N PHE K 55 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 71 through 82 removed outlier: 3.757A pdb=" N TRP K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 112 Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU K 116 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE K 145 " --> pdb=" O TYR K 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP K 146 " --> pdb=" O PRO K 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 142 through 146' Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 167 through 210 Processing helix chain 'K' and resid 216 through 253 Processing helix chain 'K' and resid 270 through 276 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) Proline residue: L 59 - end of helix Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.751A pdb=" N TRP L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 112 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU L 116 " --> pdb=" O VAL L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE L 145 " --> pdb=" O TYR L 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP L 146 " --> pdb=" O PRO L 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 142 through 146' Processing helix chain 'L' and resid 149 through 159 Processing helix chain 'L' and resid 167 through 210 Processing helix chain 'L' and resid 216 through 253 Processing helix chain 'L' and resid 270 through 276 Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 15 through 38 removed outlier: 3.628A pdb=" N ILE M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 70 removed outlier: 3.970A pdb=" N PHE M 55 " --> pdb=" O TYR M 51 " (cutoff:3.500A) Proline residue: M 59 - end of helix Processing helix chain 'M' and resid 71 through 82 removed outlier: 3.750A pdb=" N TRP M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 112 Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU M 116 " --> pdb=" O VAL M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 146 removed outlier: 3.693A pdb=" N PHE M 145 " --> pdb=" O TYR M 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP M 146 " --> pdb=" O PRO M 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 142 through 146' Processing helix chain 'M' and resid 149 through 159 Processing helix chain 'M' and resid 167 through 210 Processing helix chain 'M' and resid 216 through 253 Processing helix chain 'M' and resid 270 through 276 Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE N 19 " --> pdb=" O ASN N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) Proline residue: N 59 - end of helix Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.751A pdb=" N TRP N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 112 Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.549A pdb=" N LEU N 116 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS N 131 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE N 145 " --> pdb=" O TYR N 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP N 146 " --> pdb=" O PRO N 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 142 through 146' Processing helix chain 'N' and resid 149 through 159 Processing helix chain 'N' and resid 167 through 210 Processing helix chain 'N' and resid 216 through 253 Processing helix chain 'N' and resid 270 through 276 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 15 through 38 removed outlier: 3.628A pdb=" N ILE O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE O 55 " --> pdb=" O TYR O 51 " (cutoff:3.500A) Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 71 through 82 removed outlier: 3.750A pdb=" N TRP O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 112 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.549A pdb=" N LEU O 116 " --> pdb=" O VAL O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 4.107A pdb=" N CYS O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 146 removed outlier: 3.693A pdb=" N PHE O 145 " --> pdb=" O TYR O 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP O 146 " --> pdb=" O PRO O 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 142 through 146' Processing helix chain 'O' and resid 149 through 159 Processing helix chain 'O' and resid 167 through 210 Processing helix chain 'O' and resid 216 through 253 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE P 19 " --> pdb=" O ASN P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) Proline residue: P 59 - end of helix Processing helix chain 'P' and resid 71 through 82 removed outlier: 3.750A pdb=" N TRP P 75 " --> pdb=" O ARG P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 112 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU P 116 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 133 removed outlier: 4.107A pdb=" N CYS P 131 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE P 145 " --> pdb=" O TYR P 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP P 146 " --> pdb=" O PRO P 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 142 through 146' Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 167 through 210 Processing helix chain 'P' and resid 216 through 253 Processing helix chain 'P' and resid 270 through 276 Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 15 through 38 removed outlier: 3.628A pdb=" N ILE Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 70 removed outlier: 3.970A pdb=" N PHE Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) Proline residue: Q 59 - end of helix Processing helix chain 'Q' and resid 71 through 82 removed outlier: 3.751A pdb=" N TRP Q 75 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 112 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 4.105A pdb=" N CYS Q 131 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 146 removed outlier: 3.693A pdb=" N PHE Q 145 " --> pdb=" O TYR Q 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP Q 146 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 142 through 146' Processing helix chain 'Q' and resid 149 through 159 Processing helix chain 'Q' and resid 167 through 210 Processing helix chain 'Q' and resid 216 through 253 Processing helix chain 'Q' and resid 270 through 276 Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE R 19 " --> pdb=" O ASN R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE R 55 " --> pdb=" O TYR R 51 " (cutoff:3.500A) Proline residue: R 59 - end of helix Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.752A pdb=" N TRP R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 112 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU R 116 " --> pdb=" O VAL R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS R 131 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE R 145 " --> pdb=" O TYR R 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP R 146 " --> pdb=" O PRO R 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 142 through 146' Processing helix chain 'R' and resid 149 through 159 Processing helix chain 'R' and resid 167 through 210 Processing helix chain 'R' and resid 216 through 253 Processing helix chain 'R' and resid 270 through 276 Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 15 through 38 removed outlier: 3.628A pdb=" N ILE S 19 " --> pdb=" O ASN S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE S 55 " --> pdb=" O TYR S 51 " (cutoff:3.500A) Proline residue: S 59 - end of helix Processing helix chain 'S' and resid 71 through 82 removed outlier: 3.751A pdb=" N TRP S 75 " --> pdb=" O ARG S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 112 Processing helix chain 'S' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU S 116 " --> pdb=" O VAL S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS S 131 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE S 145 " --> pdb=" O TYR S 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP S 146 " --> pdb=" O PRO S 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 142 through 146' Processing helix chain 'S' and resid 149 through 159 Processing helix chain 'S' and resid 167 through 210 Processing helix chain 'S' and resid 216 through 253 Processing helix chain 'S' and resid 270 through 276 Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE T 19 " --> pdb=" O ASN T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE T 55 " --> pdb=" O TYR T 51 " (cutoff:3.500A) Proline residue: T 59 - end of helix Processing helix chain 'T' and resid 71 through 82 removed outlier: 3.751A pdb=" N TRP T 75 " --> pdb=" O ARG T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 112 Processing helix chain 'T' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU T 116 " --> pdb=" O VAL T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS T 131 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE T 145 " --> pdb=" O TYR T 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP T 146 " --> pdb=" O PRO T 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 142 through 146' Processing helix chain 'T' and resid 149 through 159 Processing helix chain 'T' and resid 167 through 210 Processing helix chain 'T' and resid 216 through 253 Processing helix chain 'T' and resid 270 through 276 Processing helix chain 'U' and resid 5 through 15 Processing helix chain 'U' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE U 19 " --> pdb=" O ASN U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE U 55 " --> pdb=" O TYR U 51 " (cutoff:3.500A) Proline residue: U 59 - end of helix Processing helix chain 'U' and resid 71 through 82 removed outlier: 3.750A pdb=" N TRP U 75 " --> pdb=" O ARG U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 112 Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU U 116 " --> pdb=" O VAL U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS U 131 " --> pdb=" O THR U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE U 145 " --> pdb=" O TYR U 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP U 146 " --> pdb=" O PRO U 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 142 through 146' Processing helix chain 'U' and resid 149 through 159 Processing helix chain 'U' and resid 167 through 210 Processing helix chain 'U' and resid 216 through 253 Processing helix chain 'U' and resid 270 through 276 Processing helix chain 'V' and resid 5 through 15 Processing helix chain 'V' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE V 19 " --> pdb=" O ASN V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE V 55 " --> pdb=" O TYR V 51 " (cutoff:3.500A) Proline residue: V 59 - end of helix Processing helix chain 'V' and resid 71 through 82 removed outlier: 3.751A pdb=" N TRP V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 95 through 112 Processing helix chain 'V' and resid 112 through 126 removed outlier: 3.547A pdb=" N LEU V 116 " --> pdb=" O VAL V 112 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS V 131 " --> pdb=" O THR V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE V 145 " --> pdb=" O TYR V 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP V 146 " --> pdb=" O PRO V 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 142 through 146' Processing helix chain 'V' and resid 149 through 159 Processing helix chain 'V' and resid 167 through 210 Processing helix chain 'V' and resid 216 through 253 Processing helix chain 'V' and resid 270 through 276 3498 hydrogen bonds defined for protein. 10494 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: 15.13 Time building geometry restraints manager: 20.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 14454 1.35 - 1.47: 11828 1.47 - 1.59: 20006 1.59 - 1.72: 0 1.72 - 1.84: 550 Bond restraints: 46838 Sorted by residual: bond pdb=" CG GLU Q 259 " pdb=" CD GLU Q 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.73e+00 bond pdb=" CG GLU T 259 " pdb=" CD GLU T 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.72e+00 bond pdb=" CG GLU P 259 " pdb=" CD GLU P 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.67e+00 bond pdb=" CG GLU O 259 " pdb=" CD GLU O 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.67e+00 bond pdb=" CG GLU L 259 " pdb=" CD GLU L 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.65e+00 ... (remaining 46833 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.86: 1337 106.86 - 113.66: 27173 113.66 - 120.46: 18988 120.46 - 127.26: 15548 127.26 - 134.06: 556 Bond angle restraints: 63602 Sorted by residual: angle pdb=" C SER R 258 " pdb=" N GLU R 259 " pdb=" CA GLU R 259 " ideal model delta sigma weight residual 122.29 127.32 -5.03 1.65e+00 3.67e-01 9.31e+00 angle pdb=" C SER L 258 " pdb=" N GLU L 259 " pdb=" CA GLU L 259 " ideal model delta sigma weight residual 122.29 127.31 -5.02 1.65e+00 3.67e-01 9.26e+00 angle pdb=" C SER N 258 " pdb=" N GLU N 259 " pdb=" CA GLU N 259 " ideal model delta sigma weight residual 122.29 127.31 -5.02 1.65e+00 3.67e-01 9.25e+00 angle pdb=" C SER O 258 " pdb=" N GLU O 259 " pdb=" CA GLU O 259 " ideal model delta sigma weight residual 122.29 127.29 -5.00 1.65e+00 3.67e-01 9.20e+00 angle pdb=" C SER P 258 " pdb=" N GLU P 259 " pdb=" CA GLU P 259 " ideal model delta sigma weight residual 122.29 127.29 -5.00 1.65e+00 3.67e-01 9.19e+00 ... (remaining 63597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 25046 17.13 - 34.26: 2234 34.26 - 51.39: 583 51.39 - 68.52: 55 68.52 - 85.65: 66 Dihedral angle restraints: 27984 sinusoidal: 10802 harmonic: 17182 Sorted by residual: dihedral pdb=" CB CYS M 43 " pdb=" SG CYS M 43 " pdb=" SG CYS M 162 " pdb=" CB CYS M 162 " ideal model delta sinusoidal sigma weight residual -86.00 -171.65 85.65 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 162 " pdb=" CB CYS R 162 " ideal model delta sinusoidal sigma weight residual -86.00 -171.65 85.65 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS V 43 " pdb=" SG CYS V 43 " pdb=" SG CYS V 162 " pdb=" CB CYS V 162 " ideal model delta sinusoidal sigma weight residual -86.00 -171.65 85.65 1 1.00e+01 1.00e-02 8.87e+01 ... (remaining 27981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4910 0.038 - 0.075: 1950 0.075 - 0.113: 360 0.113 - 0.150: 161 0.150 - 0.188: 33 Chirality restraints: 7414 Sorted by residual: chirality pdb=" CA GLU L 259 " pdb=" N GLU L 259 " pdb=" C GLU L 259 " pdb=" CB GLU L 259 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA GLU Q 259 " pdb=" N GLU Q 259 " pdb=" C GLU Q 259 " pdb=" CB GLU Q 259 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA GLU S 259 " pdb=" N GLU S 259 " pdb=" C GLU S 259 " pdb=" CB GLU S 259 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.56e-01 ... (remaining 7411 not shown) Planarity restraints: 7898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU O 259 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C GLU O 259 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU O 259 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP O 260 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 259 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C GLU R 259 " 0.054 2.00e-02 2.50e+03 pdb=" O GLU R 259 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP R 260 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 259 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C GLU T 259 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU T 259 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP T 260 " -0.018 2.00e-02 2.50e+03 ... (remaining 7895 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 19248 2.91 - 3.40: 51405 3.40 - 3.90: 70761 3.90 - 4.40: 74682 4.40 - 4.90: 126585 Nonbonded interactions: 342681 Sorted by model distance: nonbonded pdb=" O SER O 138 " pdb=" OG SER O 138 " model vdw 2.407 2.440 nonbonded pdb=" O SER S 138 " pdb=" OG SER S 138 " model vdw 2.407 2.440 nonbonded pdb=" O SER Q 138 " pdb=" OG SER Q 138 " model vdw 2.407 2.440 nonbonded pdb=" O SER P 138 " pdb=" OG SER P 138 " model vdw 2.408 2.440 nonbonded pdb=" O SER N 138 " pdb=" OG SER N 138 " model vdw 2.408 2.440 ... (remaining 342676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 5.540 Check model and map are aligned: 0.690 Set scattering table: 0.450 Process input model: 111.270 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.320 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 46838 Z= 0.359 Angle : 0.682 5.708 63602 Z= 0.380 Chirality : 0.043 0.188 7414 Planarity : 0.005 0.052 7898 Dihedral : 13.936 81.472 16676 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.10), residues: 5786 helix: 0.50 (0.07), residues: 4422 sheet: None (None), residues: 0 loop : -3.29 (0.13), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 221 HIS 0.004 0.001 HIS C 239 PHE 0.012 0.002 PHE R 68 TYR 0.007 0.001 TYR N 220 ARG 0.008 0.001 ARG H 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1260 time to evaluate : 5.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.8570 (m-80) cc_final: 0.8370 (m-80) REVERT: A 73 GLN cc_start: 0.8303 (mt0) cc_final: 0.7811 (tt0) REVERT: A 74 MET cc_start: 0.7875 (tmm) cc_final: 0.7561 (tmm) REVERT: A 184 GLN cc_start: 0.8591 (mt0) cc_final: 0.8369 (tt0) REVERT: A 187 MET cc_start: 0.9309 (mmp) cc_final: 0.9051 (tpp) REVERT: A 228 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 245 MET cc_start: 0.8045 (ttm) cc_final: 0.7736 (ttm) REVERT: A 249 LYS cc_start: 0.8680 (tttt) cc_final: 0.8284 (ttpp) REVERT: B 12 LEU cc_start: 0.7621 (pp) cc_final: 0.7236 (mt) REVERT: B 51 TYR cc_start: 0.9031 (t80) cc_final: 0.8477 (t80) REVERT: B 74 MET cc_start: 0.7796 (tmm) cc_final: 0.7435 (tmm) REVERT: B 155 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 237 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8401 (tm-30) REVERT: B 249 LYS cc_start: 0.8794 (tttt) cc_final: 0.8397 (ttpp) REVERT: C 12 LEU cc_start: 0.7820 (pp) cc_final: 0.7508 (mt) REVERT: C 32 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7771 (tm-30) REVERT: C 74 MET cc_start: 0.7826 (tmm) cc_final: 0.7031 (tmm) REVERT: C 208 LYS cc_start: 0.8538 (tptp) cc_final: 0.8252 (tmmt) REVERT: C 211 SER cc_start: 0.9353 (t) cc_final: 0.8525 (p) REVERT: C 237 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8385 (tm-30) REVERT: C 249 LYS cc_start: 0.8682 (tttt) cc_final: 0.8253 (ttpp) REVERT: D 7 ASN cc_start: 0.5643 (t0) cc_final: 0.5173 (p0) REVERT: D 12 LEU cc_start: 0.7769 (pp) cc_final: 0.7379 (mt) REVERT: D 74 MET cc_start: 0.7641 (tmm) cc_final: 0.7308 (tmm) REVERT: D 155 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 175 ASP cc_start: 0.8777 (t70) cc_final: 0.8357 (t0) REVERT: D 203 SER cc_start: 0.9208 (p) cc_final: 0.8971 (t) REVERT: D 273 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8212 (tptm) REVERT: E 74 MET cc_start: 0.7067 (tmm) cc_final: 0.6844 (tmm) REVERT: E 174 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7851 (tmm-80) REVERT: E 195 LEU cc_start: 0.8590 (tt) cc_final: 0.8331 (tp) REVERT: F 74 MET cc_start: 0.7556 (tmm) cc_final: 0.6889 (tmm) REVERT: F 128 TYR cc_start: 0.8976 (m-10) cc_final: 0.8712 (m-80) REVERT: F 155 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8460 (tm-30) REVERT: F 238 GLN cc_start: 0.8359 (tt0) cc_final: 0.8142 (tt0) REVERT: F 249 LYS cc_start: 0.8966 (tttt) cc_final: 0.8610 (ttpp) REVERT: G 12 LEU cc_start: 0.7679 (pp) cc_final: 0.7406 (mm) REVERT: G 74 MET cc_start: 0.7512 (tmm) cc_final: 0.7150 (tmm) REVERT: G 128 TYR cc_start: 0.8814 (m-10) cc_final: 0.8600 (m-80) REVERT: G 155 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 237 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8220 (tm-30) REVERT: H 74 MET cc_start: 0.7806 (tmm) cc_final: 0.7571 (tmm) REVERT: H 187 MET cc_start: 0.9287 (mmp) cc_final: 0.9022 (mmt) REVERT: H 208 LYS cc_start: 0.8580 (tptp) cc_final: 0.8361 (tmmt) REVERT: H 249 LYS cc_start: 0.8348 (tttt) cc_final: 0.8038 (ttpp) REVERT: H 270 GLN cc_start: 0.7784 (tp40) cc_final: 0.7510 (tp40) REVERT: H 273 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8020 (tptm) REVERT: I 116 LEU cc_start: 0.8634 (mp) cc_final: 0.8374 (tt) REVERT: I 130 GLU cc_start: 0.7523 (pp20) cc_final: 0.7273 (pp20) REVERT: I 155 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8256 (tm-30) REVERT: I 233 GLU cc_start: 0.8511 (tp30) cc_final: 0.8181 (tt0) REVERT: I 234 GLN cc_start: 0.8976 (tt0) cc_final: 0.8646 (tt0) REVERT: I 237 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8292 (tm-30) REVERT: J 51 TYR cc_start: 0.8987 (t80) cc_final: 0.8318 (t80) REVERT: J 74 MET cc_start: 0.7973 (tmm) cc_final: 0.7397 (tmm) REVERT: J 250 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8243 (tmmt) REVERT: K 74 MET cc_start: 0.7994 (tmm) cc_final: 0.7191 (tmm) REVERT: K 77 ILE cc_start: 0.9218 (mt) cc_final: 0.8984 (mt) REVERT: K 249 LYS cc_start: 0.8662 (tttt) cc_final: 0.8362 (ttpp) REVERT: L 50 TYR cc_start: 0.8634 (m-80) cc_final: 0.8217 (m-80) REVERT: L 74 MET cc_start: 0.7962 (tmm) cc_final: 0.7146 (tmm) REVERT: L 169 ASP cc_start: 0.7837 (t0) cc_final: 0.7488 (t70) REVERT: L 187 MET cc_start: 0.9467 (mmp) cc_final: 0.9129 (tpp) REVERT: L 237 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8170 (tm-30) REVERT: L 273 LYS cc_start: 0.9052 (mmtm) cc_final: 0.8599 (tptp) REVERT: M 50 TYR cc_start: 0.8649 (m-80) cc_final: 0.8430 (m-80) REVERT: M 74 MET cc_start: 0.7724 (tmm) cc_final: 0.7097 (tmm) REVERT: M 130 GLU cc_start: 0.7785 (pp20) cc_final: 0.7447 (pp20) REVERT: M 155 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8247 (tm-30) REVERT: M 233 GLU cc_start: 0.8345 (tp30) cc_final: 0.8034 (tp30) REVERT: N 73 GLN cc_start: 0.8359 (mt0) cc_final: 0.8048 (tt0) REVERT: N 74 MET cc_start: 0.8209 (tmm) cc_final: 0.7617 (tmm) REVERT: N 249 LYS cc_start: 0.8799 (tttt) cc_final: 0.8473 (ttpp) REVERT: O 74 MET cc_start: 0.7875 (tmm) cc_final: 0.7154 (tmm) REVERT: O 130 GLU cc_start: 0.7915 (pp20) cc_final: 0.7556 (pp20) REVERT: O 208 LYS cc_start: 0.8473 (tptp) cc_final: 0.8249 (tmmt) REVERT: O 237 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8407 (tm-30) REVERT: P 5 LEU cc_start: 0.4925 (mt) cc_final: 0.4596 (tt) REVERT: P 50 TYR cc_start: 0.8505 (m-80) cc_final: 0.8256 (m-80) REVERT: P 128 TYR cc_start: 0.8909 (m-10) cc_final: 0.8522 (m-80) REVERT: P 176 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7921 (tm-30) REVERT: P 203 SER cc_start: 0.9031 (p) cc_final: 0.8822 (p) REVERT: P 237 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8406 (tm-30) REVERT: P 249 LYS cc_start: 0.8734 (tttt) cc_final: 0.8459 (tmtt) REVERT: Q 74 MET cc_start: 0.7616 (tmm) cc_final: 0.7029 (tmm) REVERT: Q 237 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8395 (tm-30) REVERT: Q 249 LYS cc_start: 0.8643 (tttt) cc_final: 0.8347 (ttpp) REVERT: Q 273 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8421 (tptp) REVERT: R 74 MET cc_start: 0.7854 (tmm) cc_final: 0.7160 (tmm) REVERT: R 233 GLU cc_start: 0.8508 (tp30) cc_final: 0.8065 (tt0) REVERT: R 237 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8059 (tm-30) REVERT: R 245 MET cc_start: 0.8193 (ttm) cc_final: 0.7705 (ttm) REVERT: R 249 LYS cc_start: 0.8841 (tttt) cc_final: 0.8542 (ttpp) REVERT: R 272 TRP cc_start: 0.8836 (m100) cc_final: 0.8480 (m100) REVERT: R 273 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8547 (tptp) REVERT: S 12 LEU cc_start: 0.7914 (pp) cc_final: 0.7531 (mt) REVERT: S 31 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8682 (tm-30) REVERT: S 73 GLN cc_start: 0.8332 (mt0) cc_final: 0.8104 (tt0) REVERT: S 203 SER cc_start: 0.9271 (p) cc_final: 0.9022 (t) REVERT: S 233 GLU cc_start: 0.8175 (tp30) cc_final: 0.7968 (tt0) REVERT: S 249 LYS cc_start: 0.8632 (tttt) cc_final: 0.8166 (ttpp) REVERT: T 51 TYR cc_start: 0.8773 (t80) cc_final: 0.8214 (t80) REVERT: T 74 MET cc_start: 0.7802 (tmm) cc_final: 0.7229 (tmm) REVERT: T 251 LEU cc_start: 0.9075 (tp) cc_final: 0.8873 (tt) REVERT: U 12 LEU cc_start: 0.7661 (pp) cc_final: 0.7283 (mt) REVERT: U 184 GLN cc_start: 0.8543 (mt0) cc_final: 0.8251 (mm-40) REVERT: U 201 LEU cc_start: 0.9351 (tp) cc_final: 0.8939 (tt) REVERT: U 233 GLU cc_start: 0.8077 (tp30) cc_final: 0.7796 (tp30) REVERT: U 249 LYS cc_start: 0.8727 (tttt) cc_final: 0.8341 (ttpp) REVERT: V 32 GLN cc_start: 0.8234 (tm-30) cc_final: 0.8027 (tm-30) REVERT: V 74 MET cc_start: 0.7612 (tmm) cc_final: 0.6996 (tmm) REVERT: V 130 GLU cc_start: 0.8056 (pp20) cc_final: 0.7822 (pp20) REVERT: V 155 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8130 (tm-30) REVERT: V 225 LEU cc_start: 0.8643 (mt) cc_final: 0.8251 (mt) REVERT: V 249 LYS cc_start: 0.8654 (tttt) cc_final: 0.8430 (ttpp) REVERT: V 250 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8510 (tmmt) REVERT: V 273 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8417 (tptm) outliers start: 0 outliers final: 0 residues processed: 1260 average time/residue: 0.6232 time to fit residues: 1219.2651 Evaluate side-chains 748 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 748 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 0.9980 chunk 433 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 448 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 272 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 chunk 519 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 ASN A 227 ASN B 48 ASN B 227 ASN C 48 ASN C 227 ASN D 48 ASN E 48 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN G 48 ASN H 48 ASN H 227 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN I 226 GLN I 227 ASN J 48 ASN J 227 ASN K 48 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN M 48 ASN N 44 GLN N 48 ASN N 227 ASN O 48 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 ASN P 227 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 ASN S 44 GLN S 48 ASN T 48 ASN T 227 ASN U 48 ASN U 73 GLN V 48 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 46838 Z= 0.212 Angle : 0.555 6.550 63602 Z= 0.298 Chirality : 0.041 0.217 7414 Planarity : 0.005 0.054 7898 Dihedral : 4.025 18.012 6270 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.37 % Allowed : 5.31 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 5786 helix: 1.81 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -3.17 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 272 HIS 0.003 0.001 HIS V 224 PHE 0.016 0.001 PHE M 68 TYR 0.015 0.001 TYR P 81 ARG 0.005 0.001 ARG J 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1040 time to evaluate : 5.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7820 (pp) cc_final: 0.7603 (mt) REVERT: A 50 TYR cc_start: 0.8469 (m-80) cc_final: 0.7996 (m-10) REVERT: A 74 MET cc_start: 0.8089 (tmm) cc_final: 0.7622 (tmm) REVERT: A 77 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8724 (mp) REVERT: A 155 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 187 MET cc_start: 0.9214 (mmp) cc_final: 0.8998 (tpp) REVERT: A 237 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 249 LYS cc_start: 0.8357 (tttt) cc_final: 0.8140 (ttpp) REVERT: B 12 LEU cc_start: 0.7686 (pp) cc_final: 0.7398 (mt) REVERT: B 21 SER cc_start: 0.8777 (t) cc_final: 0.8577 (t) REVERT: B 51 TYR cc_start: 0.9074 (t80) cc_final: 0.8860 (t80) REVERT: B 74 MET cc_start: 0.8159 (tmm) cc_final: 0.7663 (tmm) REVERT: C 73 GLN cc_start: 0.8328 (mt0) cc_final: 0.8094 (mt0) REVERT: C 187 MET cc_start: 0.9129 (mmp) cc_final: 0.8910 (tpp) REVERT: C 208 LYS cc_start: 0.8473 (tptp) cc_final: 0.8193 (tmmt) REVERT: C 211 SER cc_start: 0.9380 (t) cc_final: 0.8566 (p) REVERT: C 242 LEU cc_start: 0.9186 (mm) cc_final: 0.8935 (mt) REVERT: C 249 LYS cc_start: 0.8485 (tttt) cc_final: 0.8138 (ttpp) REVERT: C 250 LYS cc_start: 0.8721 (tmmt) cc_final: 0.8166 (ttmt) REVERT: D 12 LEU cc_start: 0.7494 (pp) cc_final: 0.7287 (mt) REVERT: D 74 MET cc_start: 0.7827 (tmm) cc_final: 0.7316 (tmm) REVERT: D 155 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 175 ASP cc_start: 0.8831 (t70) cc_final: 0.8561 (t70) REVERT: D 203 SER cc_start: 0.9104 (p) cc_final: 0.8839 (t) REVERT: D 237 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8440 (tm-30) REVERT: E 74 MET cc_start: 0.7466 (tmm) cc_final: 0.6520 (tmm) REVERT: E 176 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7889 (tm-30) REVERT: E 195 LEU cc_start: 0.8615 (tt) cc_final: 0.8367 (tp) REVERT: E 249 LYS cc_start: 0.8720 (tttt) cc_final: 0.8413 (ttpp) REVERT: F 74 MET cc_start: 0.7699 (tmm) cc_final: 0.6928 (tmm) REVERT: F 155 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8567 (tm-30) REVERT: F 220 TYR cc_start: 0.8925 (t80) cc_final: 0.8713 (t80) REVERT: F 249 LYS cc_start: 0.8762 (tttt) cc_final: 0.8507 (ttpp) REVERT: G 74 MET cc_start: 0.7849 (tmm) cc_final: 0.7247 (tmm) REVERT: G 99 LEU cc_start: 0.8904 (mt) cc_final: 0.8657 (mt) REVERT: G 175 ASP cc_start: 0.8650 (t70) cc_final: 0.8214 (t70) REVERT: G 233 GLU cc_start: 0.8222 (tp30) cc_final: 0.7929 (tp30) REVERT: G 237 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8235 (tm-30) REVERT: H 73 GLN cc_start: 0.8083 (mt0) cc_final: 0.7658 (tt0) REVERT: H 99 LEU cc_start: 0.8691 (mt) cc_final: 0.7938 (pp) REVERT: H 128 TYR cc_start: 0.9061 (m-10) cc_final: 0.8781 (m-80) REVERT: H 187 MET cc_start: 0.9247 (mmp) cc_final: 0.8998 (mmt) REVERT: H 237 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8314 (tm-30) REVERT: H 250 LYS cc_start: 0.8670 (tmmt) cc_final: 0.8003 (ttmt) REVERT: H 270 GLN cc_start: 0.7657 (tp40) cc_final: 0.7349 (tp40) REVERT: I 74 MET cc_start: 0.8200 (tmm) cc_final: 0.7355 (tmm) REVERT: I 155 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8299 (tm-30) REVERT: I 250 LYS cc_start: 0.9089 (tmmt) cc_final: 0.8541 (ttmt) REVERT: J 74 MET cc_start: 0.8129 (tmm) cc_final: 0.7755 (tmm) REVERT: J 208 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8240 (tmmt) REVERT: J 250 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8152 (tmmt) REVERT: K 74 MET cc_start: 0.7953 (tmm) cc_final: 0.7428 (tmm) REVERT: K 130 GLU cc_start: 0.8337 (pp20) cc_final: 0.8069 (pp20) REVERT: K 237 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8402 (tm-30) REVERT: L 50 TYR cc_start: 0.8558 (m-80) cc_final: 0.8129 (m-80) REVERT: L 74 MET cc_start: 0.8132 (tmm) cc_final: 0.7233 (tmm) REVERT: L 144 MET cc_start: 0.8108 (pmm) cc_final: 0.7688 (pmm) REVERT: L 249 LYS cc_start: 0.8418 (tttm) cc_final: 0.7965 (ttpp) REVERT: L 273 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8412 (tptp) REVERT: M 50 TYR cc_start: 0.8498 (m-80) cc_final: 0.8256 (m-80) REVERT: M 74 MET cc_start: 0.7900 (tmm) cc_final: 0.7210 (tmm) REVERT: M 237 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8375 (tm-30) REVERT: N 74 MET cc_start: 0.8201 (tmm) cc_final: 0.7896 (tmm) REVERT: O 74 MET cc_start: 0.8042 (tmm) cc_final: 0.7284 (tmm) REVERT: O 99 LEU cc_start: 0.8966 (mt) cc_final: 0.8761 (mt) REVERT: O 128 TYR cc_start: 0.8952 (m-10) cc_final: 0.8515 (m-80) REVERT: O 176 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7966 (tm-30) REVERT: O 233 GLU cc_start: 0.8349 (tp30) cc_final: 0.8022 (tt0) REVERT: P 5 LEU cc_start: 0.5319 (mt) cc_final: 0.4898 (tt) REVERT: P 50 TYR cc_start: 0.8402 (m-80) cc_final: 0.8188 (m-80) REVERT: P 74 MET cc_start: 0.8093 (tpp) cc_final: 0.7801 (tpp) REVERT: P 116 LEU cc_start: 0.9132 (tp) cc_final: 0.8907 (tt) REVERT: P 233 GLU cc_start: 0.8251 (tp30) cc_final: 0.7948 (tp30) REVERT: P 237 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8467 (tm-30) REVERT: Q 5 LEU cc_start: 0.5795 (mt) cc_final: 0.5461 (tt) REVERT: Q 116 LEU cc_start: 0.8850 (mt) cc_final: 0.8522 (tt) REVERT: Q 233 GLU cc_start: 0.8418 (tp30) cc_final: 0.8019 (tp30) REVERT: Q 237 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8441 (tm-30) REVERT: Q 249 LYS cc_start: 0.8455 (tttt) cc_final: 0.8222 (ttpp) REVERT: R 74 MET cc_start: 0.7866 (tmm) cc_final: 0.7230 (tmm) REVERT: R 99 LEU cc_start: 0.8582 (mt) cc_final: 0.8204 (mt) REVERT: R 130 GLU cc_start: 0.7741 (pp20) cc_final: 0.7499 (pp20) REVERT: R 233 GLU cc_start: 0.8304 (tp30) cc_final: 0.8015 (tp30) REVERT: R 237 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8139 (tm-30) REVERT: R 249 LYS cc_start: 0.8622 (tttt) cc_final: 0.8361 (ttpp) REVERT: R 272 TRP cc_start: 0.8851 (m100) cc_final: 0.8452 (m100) REVERT: R 273 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8500 (tptm) REVERT: S 12 LEU cc_start: 0.7830 (pp) cc_final: 0.7591 (mt) REVERT: S 99 LEU cc_start: 0.8715 (mt) cc_final: 0.8488 (mt) REVERT: S 203 SER cc_start: 0.9261 (p) cc_final: 0.8957 (t) REVERT: S 237 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8178 (tm-30) REVERT: S 249 LYS cc_start: 0.8598 (tttt) cc_final: 0.8376 (ttpp) REVERT: T 51 TYR cc_start: 0.8857 (t80) cc_final: 0.8207 (t80) REVERT: T 74 MET cc_start: 0.8028 (tmm) cc_final: 0.7469 (tmm) REVERT: T 99 LEU cc_start: 0.8981 (mt) cc_final: 0.8765 (mt) REVERT: T 155 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8156 (tm-30) REVERT: T 208 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8271 (tmmt) REVERT: U 12 LEU cc_start: 0.7477 (pp) cc_final: 0.7193 (mt) REVERT: U 74 MET cc_start: 0.7875 (tmm) cc_final: 0.7326 (tmm) REVERT: U 128 TYR cc_start: 0.8986 (m-10) cc_final: 0.8562 (m-80) REVERT: U 155 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8256 (tm-30) REVERT: U 184 GLN cc_start: 0.8487 (mt0) cc_final: 0.8180 (mm-40) REVERT: U 201 LEU cc_start: 0.9319 (tp) cc_final: 0.9048 (tt) REVERT: U 249 LYS cc_start: 0.8507 (tttt) cc_final: 0.8287 (ttpp) REVERT: V 73 GLN cc_start: 0.8238 (mt0) cc_final: 0.7973 (mt0) REVERT: V 74 MET cc_start: 0.7949 (tmm) cc_final: 0.7114 (tmm) REVERT: V 155 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8417 (tm-30) REVERT: V 250 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8327 (tmmt) REVERT: V 273 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8191 (tptm) outliers start: 19 outliers final: 0 residues processed: 1055 average time/residue: 0.5583 time to fit residues: 963.5223 Evaluate side-chains 729 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 728 time to evaluate : 5.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 432 optimal weight: 5.9990 chunk 353 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 520 optimal weight: 3.9990 chunk 562 optimal weight: 4.9990 chunk 463 optimal weight: 0.9990 chunk 516 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 417 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN C 48 ASN E 181 HIS ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN H 227 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN N 227 ASN O 227 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN Q 227 ASN R 44 GLN S 227 ASN T 227 ASN V 44 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 46838 Z= 0.168 Angle : 0.524 5.481 63602 Z= 0.282 Chirality : 0.039 0.211 7414 Planarity : 0.005 0.054 7898 Dihedral : 3.918 19.093 6270 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.31 % Allowed : 4.72 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.11), residues: 5786 helix: 2.42 (0.08), residues: 4554 sheet: None (None), residues: 0 loop : -2.92 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 221 HIS 0.003 0.001 HIS G 224 PHE 0.015 0.001 PHE Q 232 TYR 0.012 0.001 TYR E 129 ARG 0.006 0.000 ARG P 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1022 time to evaluate : 5.062 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7744 (pp) cc_final: 0.7528 (mt) REVERT: A 50 TYR cc_start: 0.8407 (m-80) cc_final: 0.7888 (m-10) REVERT: A 74 MET cc_start: 0.8067 (tmm) cc_final: 0.7510 (tmm) REVERT: A 77 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 78 THR cc_start: 0.7694 (p) cc_final: 0.7431 (p) REVERT: B 12 LEU cc_start: 0.7571 (pp) cc_final: 0.7326 (mt) REVERT: B 74 MET cc_start: 0.8107 (tmm) cc_final: 0.7739 (tmm) REVERT: B 78 THR cc_start: 0.7287 (p) cc_final: 0.6942 (p) REVERT: B 135 GLU cc_start: 0.8229 (pp20) cc_final: 0.7841 (pp20) REVERT: B 249 LYS cc_start: 0.8218 (tmtt) cc_final: 0.7865 (ttpp) REVERT: C 12 LEU cc_start: 0.7951 (mt) cc_final: 0.7516 (pp) REVERT: C 48 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7677 (t0) REVERT: C 250 LYS cc_start: 0.8630 (tmmt) cc_final: 0.8098 (ttmt) REVERT: D 12 LEU cc_start: 0.7441 (pp) cc_final: 0.7233 (mm) REVERT: D 74 MET cc_start: 0.7831 (tmm) cc_final: 0.7311 (tmm) REVERT: D 78 THR cc_start: 0.7980 (p) cc_final: 0.7708 (p) REVERT: D 175 ASP cc_start: 0.8744 (t70) cc_final: 0.8404 (t70) REVERT: D 201 LEU cc_start: 0.9321 (tp) cc_final: 0.9067 (tp) REVERT: D 203 SER cc_start: 0.9058 (p) cc_final: 0.8858 (t) REVERT: D 227 ASN cc_start: 0.9001 (m-40) cc_final: 0.8657 (m-40) REVERT: E 74 MET cc_start: 0.7090 (tmm) cc_final: 0.6292 (tmm) REVERT: E 128 TYR cc_start: 0.8906 (m-10) cc_final: 0.8694 (m-80) REVERT: E 176 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7941 (tm-30) REVERT: F 74 MET cc_start: 0.7758 (tmm) cc_final: 0.6957 (tmm) REVERT: F 128 TYR cc_start: 0.8770 (m-80) cc_final: 0.8324 (m-80) REVERT: F 135 GLU cc_start: 0.8149 (pp20) cc_final: 0.7422 (pp20) REVERT: F 220 TYR cc_start: 0.8922 (t80) cc_final: 0.8663 (t80) REVERT: F 249 LYS cc_start: 0.8578 (tttt) cc_final: 0.8284 (ttpp) REVERT: G 99 LEU cc_start: 0.8838 (mt) cc_final: 0.8614 (mt) REVERT: G 152 LYS cc_start: 0.8973 (tptt) cc_final: 0.8672 (tptm) REVERT: H 12 LEU cc_start: 0.7586 (pp) cc_final: 0.7292 (mm) REVERT: H 73 GLN cc_start: 0.8036 (mt0) cc_final: 0.7751 (mp10) REVERT: H 74 MET cc_start: 0.7906 (tmm) cc_final: 0.7512 (tmm) REVERT: H 99 LEU cc_start: 0.8650 (mt) cc_final: 0.7817 (pp) REVERT: H 128 TYR cc_start: 0.9046 (m-10) cc_final: 0.8640 (m-80) REVERT: H 187 MET cc_start: 0.9268 (mmp) cc_final: 0.8973 (mmt) REVERT: H 237 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8226 (tm-30) REVERT: H 250 LYS cc_start: 0.8584 (tmmt) cc_final: 0.7951 (ttmt) REVERT: H 270 GLN cc_start: 0.7608 (tp40) cc_final: 0.7275 (tp40) REVERT: H 273 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7918 (mtpp) REVERT: I 74 MET cc_start: 0.7777 (tmm) cc_final: 0.7292 (tmm) REVERT: I 250 LYS cc_start: 0.8903 (tmmt) cc_final: 0.8357 (ttmt) REVERT: J 14 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8381 (mtp85) REVERT: J 32 GLN cc_start: 0.8257 (tm-30) cc_final: 0.8056 (tm-30) REVERT: J 74 MET cc_start: 0.8120 (tmm) cc_final: 0.7608 (tmm) REVERT: J 208 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8296 (tmmt) REVERT: K 74 MET cc_start: 0.7946 (tmm) cc_final: 0.7342 (tmm) REVERT: K 130 GLU cc_start: 0.8331 (pp20) cc_final: 0.8120 (pp20) REVERT: L 50 TYR cc_start: 0.8519 (m-80) cc_final: 0.8171 (m-80) REVERT: L 53 SER cc_start: 0.8404 (t) cc_final: 0.8191 (t) REVERT: L 74 MET cc_start: 0.7914 (tmm) cc_final: 0.7293 (tmm) REVERT: L 135 GLU cc_start: 0.8254 (pp20) cc_final: 0.7528 (pp20) REVERT: L 187 MET cc_start: 0.9359 (mmp) cc_final: 0.9109 (mmt) REVERT: L 237 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8222 (tm-30) REVERT: L 249 LYS cc_start: 0.8262 (tttm) cc_final: 0.7831 (ttpp) REVERT: L 273 LYS cc_start: 0.8585 (mmtm) cc_final: 0.8339 (tptp) REVERT: M 12 LEU cc_start: 0.8030 (mt) cc_final: 0.7546 (pp) REVERT: M 74 MET cc_start: 0.7760 (tmm) cc_final: 0.7115 (tmm) REVERT: N 12 LEU cc_start: 0.8135 (mm) cc_final: 0.7612 (pp) REVERT: N 74 MET cc_start: 0.8064 (tmm) cc_final: 0.7414 (tmm) REVERT: N 78 THR cc_start: 0.7634 (p) cc_final: 0.7166 (p) REVERT: N 144 MET cc_start: 0.7893 (pmm) cc_final: 0.7181 (pmm) REVERT: N 249 LYS cc_start: 0.8370 (tttm) cc_final: 0.8143 (ttpp) REVERT: O 74 MET cc_start: 0.7842 (tmm) cc_final: 0.7213 (tmm) REVERT: O 99 LEU cc_start: 0.8862 (mt) cc_final: 0.8640 (mt) REVERT: O 128 TYR cc_start: 0.8893 (m-10) cc_final: 0.8541 (m-80) REVERT: P 74 MET cc_start: 0.8352 (tpp) cc_final: 0.7992 (tpp) REVERT: P 104 PHE cc_start: 0.8302 (t80) cc_final: 0.7977 (t80) REVERT: P 135 GLU cc_start: 0.7907 (pp20) cc_final: 0.6906 (pp20) REVERT: P 237 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8418 (tm-30) REVERT: Q 74 MET cc_start: 0.8173 (tpp) cc_final: 0.7847 (tpp) REVERT: Q 116 LEU cc_start: 0.8807 (mt) cc_final: 0.8542 (tt) REVERT: Q 233 GLU cc_start: 0.8353 (tp30) cc_final: 0.8020 (tp30) REVERT: R 74 MET cc_start: 0.7884 (tmm) cc_final: 0.7374 (tmm) REVERT: R 78 THR cc_start: 0.7339 (p) cc_final: 0.7074 (p) REVERT: R 99 LEU cc_start: 0.8454 (mt) cc_final: 0.8046 (mt) REVERT: R 130 GLU cc_start: 0.7697 (pp20) cc_final: 0.7420 (pp20) REVERT: R 135 GLU cc_start: 0.8463 (pp20) cc_final: 0.8237 (pp20) REVERT: R 233 GLU cc_start: 0.8312 (tp30) cc_final: 0.8020 (tp30) REVERT: R 237 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8091 (tm-30) REVERT: R 249 LYS cc_start: 0.8520 (tttt) cc_final: 0.8306 (ttpp) REVERT: R 273 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8537 (tptm) REVERT: S 99 LEU cc_start: 0.8594 (mt) cc_final: 0.8377 (mt) REVERT: S 203 SER cc_start: 0.9131 (p) cc_final: 0.8853 (t) REVERT: S 237 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8297 (tm-30) REVERT: T 12 LEU cc_start: 0.7806 (pp) cc_final: 0.7436 (mt) REVERT: T 51 TYR cc_start: 0.8931 (t80) cc_final: 0.8174 (t80) REVERT: T 74 MET cc_start: 0.8024 (tmm) cc_final: 0.7378 (tmm) REVERT: T 99 LEU cc_start: 0.8810 (mt) cc_final: 0.8570 (mt) REVERT: T 208 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8181 (tmmt) REVERT: U 12 LEU cc_start: 0.7455 (pp) cc_final: 0.7174 (mt) REVERT: U 74 MET cc_start: 0.7873 (tmm) cc_final: 0.7318 (tmm) REVERT: U 128 TYR cc_start: 0.8962 (m-10) cc_final: 0.8609 (m-80) REVERT: U 201 LEU cc_start: 0.9316 (tp) cc_final: 0.9033 (tt) REVERT: U 249 LYS cc_start: 0.8453 (tttt) cc_final: 0.8205 (ttpp) REVERT: V 12 LEU cc_start: 0.7528 (pp) cc_final: 0.7282 (mt) REVERT: V 74 MET cc_start: 0.7688 (tmm) cc_final: 0.6993 (tmm) REVERT: V 135 GLU cc_start: 0.7925 (pp20) cc_final: 0.7663 (pp20) REVERT: V 174 ARG cc_start: 0.8136 (tmm-80) cc_final: 0.7771 (tmm-80) REVERT: V 250 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8285 (tmmt) outliers start: 16 outliers final: 0 residues processed: 1035 average time/residue: 0.5743 time to fit residues: 960.8313 Evaluate side-chains 730 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 728 time to evaluate : 5.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 10.0000 chunk 391 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 349 optimal weight: 0.9990 chunk 522 optimal weight: 0.9980 chunk 552 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 494 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN D 73 GLN D 226 GLN E 227 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN G 227 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 GLN Q 227 ASN S 44 GLN T 227 ASN U 227 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46838 Z= 0.211 Angle : 0.551 8.135 63602 Z= 0.295 Chirality : 0.040 0.205 7414 Planarity : 0.005 0.050 7898 Dihedral : 3.850 19.238 6270 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.24 % Allowed : 4.39 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.11), residues: 5786 helix: 2.57 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.70 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 221 HIS 0.004 0.001 HIS T 224 PHE 0.013 0.001 PHE Q 232 TYR 0.009 0.001 TYR U 183 ARG 0.013 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 972 time to evaluate : 5.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7755 (pp) cc_final: 0.7512 (mt) REVERT: A 50 TYR cc_start: 0.8409 (m-80) cc_final: 0.8194 (m-80) REVERT: A 74 MET cc_start: 0.8106 (tmm) cc_final: 0.7612 (tmm) REVERT: B 74 MET cc_start: 0.7925 (tmm) cc_final: 0.7530 (tmm) REVERT: B 116 LEU cc_start: 0.8977 (mt) cc_final: 0.8550 (tt) REVERT: C 12 LEU cc_start: 0.7986 (mt) cc_final: 0.7546 (pp) REVERT: C 99 LEU cc_start: 0.8855 (mt) cc_final: 0.8655 (mt) REVERT: C 174 ARG cc_start: 0.8367 (tmm-80) cc_final: 0.7921 (tmm-80) REVERT: D 152 LYS cc_start: 0.9161 (tptt) cc_final: 0.8948 (tptm) REVERT: D 175 ASP cc_start: 0.8715 (t70) cc_final: 0.8352 (t70) REVERT: D 228 GLU cc_start: 0.8269 (pp20) cc_final: 0.7879 (tm-30) REVERT: D 237 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8447 (tm-30) REVERT: E 74 MET cc_start: 0.7202 (tmm) cc_final: 0.6523 (tmm) REVERT: E 135 GLU cc_start: 0.8166 (pm20) cc_final: 0.7256 (pp20) REVERT: E 176 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7945 (tm-30) REVERT: E 195 LEU cc_start: 0.8647 (tt) cc_final: 0.8395 (tp) REVERT: E 249 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8129 (ttpp) REVERT: F 74 MET cc_start: 0.7645 (tmm) cc_final: 0.6936 (tmm) REVERT: F 128 TYR cc_start: 0.8857 (m-80) cc_final: 0.8477 (m-80) REVERT: F 135 GLU cc_start: 0.8105 (pp20) cc_final: 0.7630 (pp20) REVERT: F 220 TYR cc_start: 0.9030 (t80) cc_final: 0.8796 (t80) REVERT: F 249 LYS cc_start: 0.8547 (tttt) cc_final: 0.8318 (ttpp) REVERT: G 99 LEU cc_start: 0.8912 (mt) cc_final: 0.8655 (mt) REVERT: H 74 MET cc_start: 0.7925 (tmm) cc_final: 0.7465 (tmm) REVERT: H 99 LEU cc_start: 0.8696 (mt) cc_final: 0.7814 (pp) REVERT: H 128 TYR cc_start: 0.9042 (m-10) cc_final: 0.8679 (m-80) REVERT: H 176 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8115 (tm-30) REVERT: H 187 MET cc_start: 0.9309 (mmp) cc_final: 0.8952 (tpp) REVERT: H 237 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8326 (tm-30) REVERT: H 250 LYS cc_start: 0.8601 (tmmt) cc_final: 0.7907 (ttmt) REVERT: I 74 MET cc_start: 0.7907 (tmm) cc_final: 0.7335 (tmm) REVERT: J 32 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8001 (tm-30) REVERT: J 74 MET cc_start: 0.8045 (tmm) cc_final: 0.7631 (tmm) REVERT: J 208 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8308 (tmmt) REVERT: K 74 MET cc_start: 0.8102 (tmm) cc_final: 0.7520 (tmm) REVERT: K 130 GLU cc_start: 0.8306 (pp20) cc_final: 0.8040 (pp20) REVERT: L 12 LEU cc_start: 0.8127 (mt) cc_final: 0.7775 (pp) REVERT: L 50 TYR cc_start: 0.8557 (m-80) cc_final: 0.8214 (m-80) REVERT: L 74 MET cc_start: 0.7924 (tmm) cc_final: 0.7260 (tmm) REVERT: L 237 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8378 (tm-30) REVERT: L 273 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8347 (tptp) REVERT: M 12 LEU cc_start: 0.8060 (mt) cc_final: 0.7581 (pp) REVERT: M 74 MET cc_start: 0.7877 (tmm) cc_final: 0.7213 (tmm) REVERT: M 237 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8385 (tm-30) REVERT: N 12 LEU cc_start: 0.8106 (mm) cc_final: 0.7545 (pp) REVERT: N 74 MET cc_start: 0.8084 (tmm) cc_final: 0.7442 (tmm) REVERT: N 99 LEU cc_start: 0.8749 (mt) cc_final: 0.8529 (mt) REVERT: N 135 GLU cc_start: 0.8125 (pp20) cc_final: 0.7893 (pp20) REVERT: O 12 LEU cc_start: 0.7862 (mm) cc_final: 0.7540 (pp) REVERT: O 74 MET cc_start: 0.7867 (tmm) cc_final: 0.7243 (tmm) REVERT: O 99 LEU cc_start: 0.8991 (mt) cc_final: 0.8750 (mt) REVERT: O 128 TYR cc_start: 0.8896 (m-10) cc_final: 0.8556 (m-80) REVERT: P 74 MET cc_start: 0.8534 (tpp) cc_final: 0.8175 (tpp) REVERT: P 104 PHE cc_start: 0.8372 (t80) cc_final: 0.8141 (t80) REVERT: P 187 MET cc_start: 0.9275 (mmm) cc_final: 0.8855 (mmm) REVERT: P 229 ARG cc_start: 0.8481 (tpp-160) cc_final: 0.7879 (tpp80) REVERT: Q 74 MET cc_start: 0.8260 (tpp) cc_final: 0.8019 (tpp) REVERT: Q 116 LEU cc_start: 0.8854 (mt) cc_final: 0.8575 (tt) REVERT: Q 233 GLU cc_start: 0.8305 (tp30) cc_final: 0.7938 (tp30) REVERT: R 74 MET cc_start: 0.7850 (tmm) cc_final: 0.7352 (tmm) REVERT: R 99 LEU cc_start: 0.8587 (mt) cc_final: 0.8182 (mt) REVERT: R 233 GLU cc_start: 0.8289 (tp30) cc_final: 0.8002 (tp30) REVERT: R 237 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8229 (tm-30) REVERT: R 273 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8538 (tptm) REVERT: S 99 LEU cc_start: 0.8675 (mt) cc_final: 0.8445 (mt) REVERT: S 203 SER cc_start: 0.9126 (p) cc_final: 0.8840 (t) REVERT: S 237 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8351 (tm-30) REVERT: S 249 LYS cc_start: 0.8344 (tttm) cc_final: 0.7978 (ttpp) REVERT: T 12 LEU cc_start: 0.7619 (pp) cc_final: 0.7301 (mt) REVERT: T 51 TYR cc_start: 0.8875 (t80) cc_final: 0.8198 (t80) REVERT: T 74 MET cc_start: 0.7997 (tmm) cc_final: 0.7335 (tmm) REVERT: T 78 THR cc_start: 0.8008 (p) cc_final: 0.7782 (p) REVERT: T 99 LEU cc_start: 0.8844 (mt) cc_final: 0.8588 (mt) REVERT: T 208 LYS cc_start: 0.8670 (mmmm) cc_final: 0.8271 (tmmt) REVERT: U 12 LEU cc_start: 0.7455 (pp) cc_final: 0.7198 (mt) REVERT: U 74 MET cc_start: 0.7914 (tmm) cc_final: 0.7004 (tmm) REVERT: U 78 THR cc_start: 0.8031 (p) cc_final: 0.7561 (p) REVERT: U 128 TYR cc_start: 0.9029 (m-10) cc_final: 0.8648 (m-80) REVERT: U 201 LEU cc_start: 0.9352 (tp) cc_final: 0.9075 (tt) REVERT: V 12 LEU cc_start: 0.7375 (pp) cc_final: 0.7125 (mt) REVERT: V 99 LEU cc_start: 0.8985 (mt) cc_final: 0.8774 (mt) REVERT: V 187 MET cc_start: 0.9118 (mmm) cc_final: 0.8911 (mmm) REVERT: V 228 GLU cc_start: 0.8359 (pp20) cc_final: 0.7695 (tm-30) REVERT: V 249 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8233 (ttpp) REVERT: V 250 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8240 (tmmt) outliers start: 12 outliers final: 0 residues processed: 983 average time/residue: 0.5582 time to fit residues: 889.6339 Evaluate side-chains 684 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 4.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 0.7980 chunk 313 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 411 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 471 optimal weight: 5.9990 chunk 382 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 282 optimal weight: 3.9990 chunk 496 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 227 ASN C 48 ASN F 238 GLN G 227 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 227 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN Q 227 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 ASN U 227 ASN ** V 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 227 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 46838 Z= 0.234 Angle : 0.573 5.588 63602 Z= 0.307 Chirality : 0.041 0.231 7414 Planarity : 0.005 0.051 7898 Dihedral : 3.861 20.216 6270 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.22 % Allowed : 2.44 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.11), residues: 5786 helix: 2.69 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.51 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 221 HIS 0.004 0.001 HIS G 224 PHE 0.014 0.001 PHE B 145 TYR 0.016 0.001 TYR I 183 ARG 0.009 0.001 ARG L 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 917 time to evaluate : 4.690 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7779 (pp) cc_final: 0.7539 (mt) REVERT: A 20 ASN cc_start: 0.8773 (m-40) cc_final: 0.8522 (m-40) REVERT: A 74 MET cc_start: 0.8143 (tmm) cc_final: 0.7858 (tmm) REVERT: A 249 LYS cc_start: 0.8363 (tmtt) cc_final: 0.7746 (ttpp) REVERT: B 21 SER cc_start: 0.8793 (t) cc_final: 0.8583 (t) REVERT: B 74 MET cc_start: 0.7939 (tmm) cc_final: 0.7588 (tmm) REVERT: B 78 THR cc_start: 0.7727 (p) cc_final: 0.7270 (p) REVERT: B 116 LEU cc_start: 0.8951 (mt) cc_final: 0.8518 (tt) REVERT: B 152 LYS cc_start: 0.8688 (tppt) cc_final: 0.8467 (tppp) REVERT: C 12 LEU cc_start: 0.8061 (mt) cc_final: 0.7599 (pp) REVERT: D 12 LEU cc_start: 0.8171 (mm) cc_final: 0.7609 (pp) REVERT: D 175 ASP cc_start: 0.8736 (t70) cc_final: 0.8358 (t70) REVERT: D 237 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8505 (tm-30) REVERT: E 74 MET cc_start: 0.7293 (tmm) cc_final: 0.6602 (tmm) REVERT: E 99 LEU cc_start: 0.8844 (mt) cc_final: 0.8640 (mt) REVERT: E 176 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8040 (tm-30) REVERT: E 249 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8140 (ttpp) REVERT: E 255 ILE cc_start: 0.9309 (pt) cc_final: 0.8731 (pt) REVERT: F 74 MET cc_start: 0.7801 (tmm) cc_final: 0.7106 (tmm) REVERT: F 128 TYR cc_start: 0.8904 (m-80) cc_final: 0.8475 (m-80) REVERT: F 249 LYS cc_start: 0.8505 (tttt) cc_final: 0.8265 (ttpp) REVERT: G 99 LEU cc_start: 0.8946 (mt) cc_final: 0.8686 (mt) REVERT: G 273 LYS cc_start: 0.8630 (tptm) cc_final: 0.8328 (tptm) REVERT: H 99 LEU cc_start: 0.8807 (mt) cc_final: 0.8554 (mt) REVERT: H 128 TYR cc_start: 0.9094 (m-10) cc_final: 0.8723 (m-80) REVERT: H 135 GLU cc_start: 0.8321 (pm20) cc_final: 0.7651 (pp20) REVERT: H 187 MET cc_start: 0.9335 (mmp) cc_final: 0.9097 (mmt) REVERT: H 237 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8354 (tm-30) REVERT: I 12 LEU cc_start: 0.8176 (mm) cc_final: 0.7648 (pp) REVERT: I 74 MET cc_start: 0.7681 (tmm) cc_final: 0.7070 (tmm) REVERT: I 155 GLU cc_start: 0.8441 (pp20) cc_final: 0.8229 (pp20) REVERT: I 250 LYS cc_start: 0.8794 (tmmt) cc_final: 0.8105 (ttpt) REVERT: J 32 GLN cc_start: 0.8348 (tm-30) cc_final: 0.8068 (tm-30) REVERT: J 116 LEU cc_start: 0.8950 (mm) cc_final: 0.8600 (tp) REVERT: J 208 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8205 (tmmt) REVERT: K 32 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7733 (tm-30) REVERT: K 74 MET cc_start: 0.8070 (tmm) cc_final: 0.7394 (tmm) REVERT: K 78 THR cc_start: 0.7082 (p) cc_final: 0.6867 (p) REVERT: K 130 GLU cc_start: 0.8313 (pp20) cc_final: 0.8034 (pp20) REVERT: K 174 ARG cc_start: 0.8361 (ttp80) cc_final: 0.7582 (tmm-80) REVERT: L 12 LEU cc_start: 0.8148 (mt) cc_final: 0.7759 (pp) REVERT: L 50 TYR cc_start: 0.8502 (m-80) cc_final: 0.8202 (m-80) REVERT: L 74 MET cc_start: 0.8033 (tmm) cc_final: 0.7402 (tmm) REVERT: L 273 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8257 (tptp) REVERT: M 12 LEU cc_start: 0.8067 (mt) cc_final: 0.7575 (pp) REVERT: M 74 MET cc_start: 0.7934 (tmm) cc_final: 0.7275 (tmm) REVERT: M 237 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8395 (tm-30) REVERT: N 12 LEU cc_start: 0.8058 (mm) cc_final: 0.7541 (pp) REVERT: N 74 MET cc_start: 0.8070 (tmm) cc_final: 0.7723 (tpt) REVERT: N 77 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8921 (mp) REVERT: N 144 MET cc_start: 0.7864 (pmm) cc_final: 0.7235 (pmm) REVERT: O 12 LEU cc_start: 0.7977 (mm) cc_final: 0.7618 (pp) REVERT: O 74 MET cc_start: 0.7828 (tmm) cc_final: 0.7263 (tmm) REVERT: O 99 LEU cc_start: 0.8991 (mt) cc_final: 0.8779 (mt) REVERT: O 128 TYR cc_start: 0.8942 (m-10) cc_final: 0.8573 (m-80) REVERT: P 12 LEU cc_start: 0.7802 (mt) cc_final: 0.7414 (pp) REVERT: P 74 MET cc_start: 0.8599 (tpp) cc_final: 0.8083 (tpp) REVERT: P 187 MET cc_start: 0.9345 (mmm) cc_final: 0.9078 (mmm) REVERT: Q 74 MET cc_start: 0.8179 (tpp) cc_final: 0.7859 (tpp) REVERT: Q 116 LEU cc_start: 0.8822 (mt) cc_final: 0.8501 (tt) REVERT: R 74 MET cc_start: 0.7914 (tmm) cc_final: 0.7368 (tmm) REVERT: R 78 THR cc_start: 0.7310 (p) cc_final: 0.6731 (p) REVERT: R 99 LEU cc_start: 0.8655 (mt) cc_final: 0.8293 (mt) REVERT: R 237 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8295 (tm-30) REVERT: R 273 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8478 (tptm) REVERT: S 53 SER cc_start: 0.8728 (t) cc_final: 0.8519 (t) REVERT: S 99 LEU cc_start: 0.8725 (mt) cc_final: 0.8490 (mt) REVERT: S 237 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8301 (tm-30) REVERT: T 12 LEU cc_start: 0.7679 (pp) cc_final: 0.7346 (mt) REVERT: T 74 MET cc_start: 0.7881 (tmm) cc_final: 0.7569 (tpp) REVERT: T 99 LEU cc_start: 0.8855 (mt) cc_final: 0.8588 (mt) REVERT: T 208 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8258 (tmmt) REVERT: T 249 LYS cc_start: 0.8317 (tttm) cc_final: 0.8011 (ttpp) REVERT: T 264 ILE cc_start: 0.9010 (mt) cc_final: 0.8764 (mm) REVERT: U 74 MET cc_start: 0.7936 (tmm) cc_final: 0.6984 (tmm) REVERT: U 81 TYR cc_start: 0.6084 (t80) cc_final: 0.5824 (t80) REVERT: U 128 TYR cc_start: 0.9075 (m-10) cc_final: 0.8722 (m-80) REVERT: U 201 LEU cc_start: 0.9389 (tp) cc_final: 0.8990 (tt) REVERT: V 12 LEU cc_start: 0.7462 (pp) cc_final: 0.7243 (mt) REVERT: V 99 LEU cc_start: 0.8987 (mt) cc_final: 0.8773 (mt) REVERT: V 187 MET cc_start: 0.9141 (mmm) cc_final: 0.8924 (mmm) REVERT: V 249 LYS cc_start: 0.8665 (tmtt) cc_final: 0.8078 (ttpp) REVERT: V 250 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8281 (tmmt) outliers start: 11 outliers final: 0 residues processed: 927 average time/residue: 0.5579 time to fit residues: 837.3139 Evaluate side-chains 700 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 699 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 3.9990 chunk 497 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 553 optimal weight: 5.9990 chunk 459 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 ASN E 227 ASN F 44 GLN ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN J 44 GLN J 227 ASN M 227 ASN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN R 227 ASN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 227 ASN U 44 GLN U 48 ASN V 44 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 46838 Z= 0.268 Angle : 0.595 6.535 63602 Z= 0.317 Chirality : 0.042 0.218 7414 Planarity : 0.005 0.050 7898 Dihedral : 3.909 20.995 6270 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.11), residues: 5786 helix: 2.68 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.61 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 221 HIS 0.006 0.001 HIS H 224 PHE 0.014 0.002 PHE F 136 TYR 0.019 0.001 TYR H 183 ARG 0.007 0.000 ARG L 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 890 time to evaluate : 5.635 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7803 (pp) cc_final: 0.7557 (mt) REVERT: A 20 ASN cc_start: 0.8955 (m-40) cc_final: 0.8719 (m-40) REVERT: A 74 MET cc_start: 0.7997 (tmm) cc_final: 0.7739 (tmm) REVERT: A 116 LEU cc_start: 0.8826 (tp) cc_final: 0.8500 (tt) REVERT: A 187 MET cc_start: 0.9336 (mmp) cc_final: 0.9106 (tpp) REVERT: B 74 MET cc_start: 0.7884 (tmm) cc_final: 0.7517 (tmm) REVERT: B 78 THR cc_start: 0.7721 (p) cc_final: 0.7247 (p) REVERT: B 135 GLU cc_start: 0.8382 (pp20) cc_final: 0.8091 (pp20) REVERT: C 12 LEU cc_start: 0.8061 (mt) cc_final: 0.7579 (pp) REVERT: D 12 LEU cc_start: 0.8295 (mm) cc_final: 0.7762 (pp) REVERT: E 74 MET cc_start: 0.7368 (tmm) cc_final: 0.6626 (tmm) REVERT: E 228 GLU cc_start: 0.8078 (pp20) cc_final: 0.7763 (tm-30) REVERT: E 249 LYS cc_start: 0.8856 (tmtt) cc_final: 0.8190 (ttpp) REVERT: F 12 LEU cc_start: 0.8086 (mt) cc_final: 0.7545 (pp) REVERT: F 74 MET cc_start: 0.7887 (tmm) cc_final: 0.7406 (tmm) REVERT: F 249 LYS cc_start: 0.8560 (tttt) cc_final: 0.8327 (ttpp) REVERT: F 271 ASP cc_start: 0.8854 (m-30) cc_final: 0.8612 (m-30) REVERT: G 74 MET cc_start: 0.8653 (tpp) cc_final: 0.8412 (tpp) REVERT: G 99 LEU cc_start: 0.8985 (mt) cc_final: 0.8747 (mt) REVERT: G 273 LYS cc_start: 0.8689 (tptm) cc_final: 0.8258 (tptm) REVERT: H 12 LEU cc_start: 0.8249 (mm) cc_final: 0.7827 (pp) REVERT: H 99 LEU cc_start: 0.8830 (mt) cc_final: 0.8604 (mt) REVERT: H 128 TYR cc_start: 0.9038 (m-10) cc_final: 0.8833 (m-80) REVERT: H 201 LEU cc_start: 0.9350 (tp) cc_final: 0.9148 (tt) REVERT: H 237 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8380 (tm-30) REVERT: I 12 LEU cc_start: 0.8189 (mm) cc_final: 0.7655 (pp) REVERT: I 74 MET cc_start: 0.7917 (tmm) cc_final: 0.7241 (tmm) REVERT: I 242 LEU cc_start: 0.9205 (mm) cc_final: 0.8957 (mt) REVERT: I 250 LYS cc_start: 0.8749 (tmmt) cc_final: 0.7989 (ttpt) REVERT: J 32 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7947 (tm-30) REVERT: J 74 MET cc_start: 0.8052 (tmm) cc_final: 0.7583 (tmm) REVERT: J 176 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8155 (tm-30) REVERT: J 208 LYS cc_start: 0.8738 (mmmm) cc_final: 0.8161 (tmmt) REVERT: K 32 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7640 (tm-30) REVERT: K 74 MET cc_start: 0.7869 (tmm) cc_final: 0.7258 (tmm) REVERT: K 78 THR cc_start: 0.7132 (p) cc_final: 0.6732 (p) REVERT: K 130 GLU cc_start: 0.8322 (pp20) cc_final: 0.8026 (pp20) REVERT: L 12 LEU cc_start: 0.8203 (mt) cc_final: 0.7769 (pp) REVERT: L 135 GLU cc_start: 0.8326 (pp20) cc_final: 0.8078 (pp20) REVERT: L 187 MET cc_start: 0.9373 (mmp) cc_final: 0.9143 (mmt) REVERT: L 237 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8343 (tm-30) REVERT: L 249 LYS cc_start: 0.8203 (tmtt) cc_final: 0.7650 (ttpp) REVERT: L 273 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8283 (tptp) REVERT: M 12 LEU cc_start: 0.8083 (mt) cc_final: 0.7580 (pp) REVERT: M 22 LEU cc_start: 0.9029 (tp) cc_final: 0.8680 (tp) REVERT: M 74 MET cc_start: 0.7939 (tmm) cc_final: 0.7337 (tmm) REVERT: N 12 LEU cc_start: 0.8085 (mm) cc_final: 0.7531 (pp) REVERT: N 78 THR cc_start: 0.7631 (p) cc_final: 0.7390 (p) REVERT: N 249 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8105 (ttpp) REVERT: O 12 LEU cc_start: 0.8011 (mm) cc_final: 0.7637 (pp) REVERT: O 74 MET cc_start: 0.7890 (tmm) cc_final: 0.7277 (tmm) REVERT: O 78 THR cc_start: 0.7093 (p) cc_final: 0.6891 (p) REVERT: O 128 TYR cc_start: 0.8960 (m-10) cc_final: 0.8580 (m-80) REVERT: P 12 LEU cc_start: 0.7821 (mt) cc_final: 0.7521 (pp) REVERT: P 74 MET cc_start: 0.8570 (tpp) cc_final: 0.8140 (tpp) REVERT: P 175 ASP cc_start: 0.8479 (t70) cc_final: 0.8158 (t70) REVERT: Q 116 LEU cc_start: 0.8791 (mt) cc_final: 0.8445 (tt) REVERT: Q 130 GLU cc_start: 0.8271 (pp20) cc_final: 0.7914 (pp20) REVERT: R 74 MET cc_start: 0.7812 (tmm) cc_final: 0.7284 (tmm) REVERT: R 99 LEU cc_start: 0.8734 (mt) cc_final: 0.8394 (mt) REVERT: R 237 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8234 (tm-30) REVERT: R 249 LYS cc_start: 0.8447 (tttm) cc_final: 0.8170 (ttpp) REVERT: R 273 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8476 (tptm) REVERT: S 99 LEU cc_start: 0.8774 (mt) cc_final: 0.8545 (mt) REVERT: S 187 MET cc_start: 0.9375 (mmp) cc_final: 0.9160 (mmm) REVERT: S 237 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8321 (tm-30) REVERT: T 12 LEU cc_start: 0.7728 (pp) cc_final: 0.7387 (mt) REVERT: T 74 MET cc_start: 0.7935 (tmm) cc_final: 0.7235 (tmm) REVERT: T 78 THR cc_start: 0.7997 (p) cc_final: 0.7781 (p) REVERT: T 99 LEU cc_start: 0.8847 (mt) cc_final: 0.8611 (mt) REVERT: T 208 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8281 (tmmt) REVERT: T 249 LYS cc_start: 0.8438 (tttm) cc_final: 0.8104 (ttpp) REVERT: U 12 LEU cc_start: 0.7912 (mt) cc_final: 0.7414 (pp) REVERT: U 128 TYR cc_start: 0.9092 (m-10) cc_final: 0.8756 (m-80) REVERT: U 201 LEU cc_start: 0.9426 (tp) cc_final: 0.9063 (tt) REVERT: U 249 LYS cc_start: 0.8280 (tttm) cc_final: 0.7963 (ttpp) REVERT: V 12 LEU cc_start: 0.7501 (pp) cc_final: 0.7259 (mt) REVERT: V 249 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8148 (ttpp) REVERT: V 250 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8317 (tmmt) outliers start: 1 outliers final: 0 residues processed: 891 average time/residue: 0.5610 time to fit residues: 811.4923 Evaluate side-chains 681 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 4.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 315 optimal weight: 7.9990 chunk 404 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 465 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 551 optimal weight: 0.8980 chunk 345 optimal weight: 7.9990 chunk 336 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN C 48 ASN C 238 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN H 44 GLN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN J 227 ASN Q 44 GLN R 227 ASN S 44 GLN S 227 ASN T 48 ASN U 48 ASN U 227 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46838 Z= 0.180 Angle : 0.552 6.947 63602 Z= 0.292 Chirality : 0.040 0.214 7414 Planarity : 0.004 0.050 7898 Dihedral : 3.820 19.925 6270 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.06 % Allowed : 1.46 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.11), residues: 5786 helix: 2.84 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.51 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 221 HIS 0.004 0.001 HIS N 224 PHE 0.013 0.001 PHE A 136 TYR 0.024 0.001 TYR M 183 ARG 0.005 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 912 time to evaluate : 5.307 Fit side-chains revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7738 (pp) cc_final: 0.7520 (mt) REVERT: A 74 MET cc_start: 0.7958 (tmm) cc_final: 0.7664 (tmm) REVERT: A 78 THR cc_start: 0.7899 (p) cc_final: 0.7405 (p) REVERT: A 116 LEU cc_start: 0.8822 (tp) cc_final: 0.8507 (tt) REVERT: B 21 SER cc_start: 0.8754 (t) cc_final: 0.8549 (t) REVERT: B 78 THR cc_start: 0.7445 (p) cc_final: 0.7064 (p) REVERT: B 116 LEU cc_start: 0.8888 (mt) cc_final: 0.8386 (tt) REVERT: B 249 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7797 (ttpp) REVERT: C 12 LEU cc_start: 0.8118 (mt) cc_final: 0.7645 (pp) REVERT: C 187 MET cc_start: 0.9291 (mmp) cc_final: 0.8895 (tpp) REVERT: D 12 LEU cc_start: 0.8241 (mm) cc_final: 0.7717 (pp) REVERT: E 74 MET cc_start: 0.7262 (tmm) cc_final: 0.6668 (tpp) REVERT: E 135 GLU cc_start: 0.8350 (pm20) cc_final: 0.7907 (pp20) REVERT: E 249 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8172 (ttpp) REVERT: F 12 LEU cc_start: 0.8045 (mt) cc_final: 0.7509 (pp) REVERT: F 74 MET cc_start: 0.7917 (tmm) cc_final: 0.7379 (tmm) REVERT: F 116 LEU cc_start: 0.8967 (tp) cc_final: 0.8639 (tt) REVERT: F 231 LEU cc_start: 0.8967 (mm) cc_final: 0.8729 (mm) REVERT: F 249 LYS cc_start: 0.8426 (tttt) cc_final: 0.8191 (ttpp) REVERT: G 99 LEU cc_start: 0.8913 (mt) cc_final: 0.8671 (mt) REVERT: G 273 LYS cc_start: 0.8616 (tptm) cc_final: 0.8105 (tptm) REVERT: H 12 LEU cc_start: 0.8207 (mm) cc_final: 0.7656 (pp) REVERT: H 73 GLN cc_start: 0.8110 (mt0) cc_final: 0.7528 (mp10) REVERT: H 99 LEU cc_start: 0.8758 (mt) cc_final: 0.8493 (mt) REVERT: H 187 MET cc_start: 0.9320 (mmp) cc_final: 0.9040 (mmt) REVERT: H 237 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8298 (tm-30) REVERT: H 270 GLN cc_start: 0.7836 (tp40) cc_final: 0.7268 (tp40) REVERT: I 12 LEU cc_start: 0.8134 (mm) cc_final: 0.7609 (pp) REVERT: I 74 MET cc_start: 0.7832 (tmm) cc_final: 0.7150 (tmm) REVERT: I 242 LEU cc_start: 0.9117 (mm) cc_final: 0.8745 (mt) REVERT: I 250 LYS cc_start: 0.8643 (tmmt) cc_final: 0.7914 (ttpt) REVERT: J 32 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7979 (tm-30) REVERT: J 74 MET cc_start: 0.7952 (tmm) cc_final: 0.7514 (tmm) REVERT: J 208 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8081 (tmmt) REVERT: K 32 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7765 (tm-30) REVERT: K 74 MET cc_start: 0.7741 (tmm) cc_final: 0.7159 (tmm) REVERT: K 130 GLU cc_start: 0.8269 (pp20) cc_final: 0.7985 (pp20) REVERT: L 12 LEU cc_start: 0.8185 (mt) cc_final: 0.7757 (pp) REVERT: L 50 TYR cc_start: 0.8469 (m-80) cc_final: 0.8237 (m-10) REVERT: L 99 LEU cc_start: 0.8800 (mt) cc_final: 0.8574 (mt) REVERT: L 135 GLU cc_start: 0.8355 (pp20) cc_final: 0.8055 (pp20) REVERT: L 237 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8251 (tm-30) REVERT: L 249 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7673 (ttpp) REVERT: M 12 LEU cc_start: 0.8093 (mt) cc_final: 0.7568 (pp) REVERT: M 74 MET cc_start: 0.7782 (tmm) cc_final: 0.7514 (tmm) REVERT: N 12 LEU cc_start: 0.8089 (mm) cc_final: 0.7560 (pp) REVERT: N 135 GLU cc_start: 0.8164 (pp20) cc_final: 0.7688 (pp20) REVERT: N 144 MET cc_start: 0.7818 (pmm) cc_final: 0.7344 (pmm) REVERT: N 249 LYS cc_start: 0.8696 (tmtt) cc_final: 0.8077 (ttpp) REVERT: O 12 LEU cc_start: 0.8005 (mm) cc_final: 0.7609 (pp) REVERT: O 74 MET cc_start: 0.7795 (tmm) cc_final: 0.7190 (tmm) REVERT: O 128 TYR cc_start: 0.8899 (m-10) cc_final: 0.8569 (m-80) REVERT: P 12 LEU cc_start: 0.7691 (mt) cc_final: 0.7379 (pp) REVERT: P 74 MET cc_start: 0.8544 (tpp) cc_final: 0.8120 (tpp) REVERT: P 273 LYS cc_start: 0.8423 (mptt) cc_final: 0.8200 (mmtt) REVERT: Q 116 LEU cc_start: 0.8720 (mt) cc_final: 0.8423 (tt) REVERT: Q 130 GLU cc_start: 0.8168 (pp20) cc_final: 0.7916 (pp20) REVERT: R 5 LEU cc_start: 0.5461 (mt) cc_final: 0.5258 (mp) REVERT: R 74 MET cc_start: 0.7762 (tmm) cc_final: 0.7265 (tmm) REVERT: R 99 LEU cc_start: 0.8619 (mt) cc_final: 0.8296 (mt) REVERT: R 249 LYS cc_start: 0.8414 (tttm) cc_final: 0.8113 (ttpp) REVERT: R 273 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8424 (tptm) REVERT: S 53 SER cc_start: 0.8739 (t) cc_final: 0.8523 (t) REVERT: S 187 MET cc_start: 0.9384 (mmp) cc_final: 0.9157 (mmm) REVERT: S 237 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8295 (tm-30) REVERT: T 12 LEU cc_start: 0.7697 (pp) cc_final: 0.7362 (mt) REVERT: T 48 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7401 (t0) REVERT: T 99 LEU cc_start: 0.8794 (mt) cc_final: 0.8545 (mt) REVERT: T 208 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8268 (tmmt) REVERT: T 249 LYS cc_start: 0.8345 (tttm) cc_final: 0.8046 (ttpp) REVERT: U 12 LEU cc_start: 0.7898 (mt) cc_final: 0.7353 (pp) REVERT: U 74 MET cc_start: 0.7779 (tmm) cc_final: 0.7443 (tmm) REVERT: U 128 TYR cc_start: 0.9036 (m-10) cc_final: 0.8744 (m-80) REVERT: U 201 LEU cc_start: 0.9398 (tp) cc_final: 0.9024 (tt) REVERT: U 227 ASN cc_start: 0.8672 (m-40) cc_final: 0.8428 (m-40) REVERT: U 249 LYS cc_start: 0.8253 (tttm) cc_final: 0.7943 (ttpp) REVERT: V 187 MET cc_start: 0.9245 (mmm) cc_final: 0.8862 (mmm) REVERT: V 225 LEU cc_start: 0.8555 (mt) cc_final: 0.8262 (mt) REVERT: V 249 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8077 (ttpp) REVERT: V 250 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8265 (tmmt) outliers start: 3 outliers final: 0 residues processed: 915 average time/residue: 0.5672 time to fit residues: 842.8685 Evaluate side-chains 659 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 658 time to evaluate : 5.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 329 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 350 optimal weight: 8.9990 chunk 375 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 433 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 238 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 ASN ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN M 227 ASN N 44 GLN R 44 GLN T 227 ASN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN V 44 GLN V 227 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 46838 Z= 0.179 Angle : 0.553 6.570 63602 Z= 0.292 Chirality : 0.040 0.224 7414 Planarity : 0.004 0.054 7898 Dihedral : 3.774 19.536 6270 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.11), residues: 5786 helix: 2.88 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.46 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 118 HIS 0.003 0.001 HIS D 224 PHE 0.012 0.001 PHE F 232 TYR 0.024 0.001 TYR R 183 ARG 0.007 0.000 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 876 time to evaluate : 5.219 Fit side-chains REVERT: A 5 LEU cc_start: 0.5451 (pt) cc_final: 0.5081 (mt) REVERT: A 12 LEU cc_start: 0.7724 (pp) cc_final: 0.7524 (mt) REVERT: A 74 MET cc_start: 0.7752 (tmm) cc_final: 0.7516 (tmm) REVERT: A 116 LEU cc_start: 0.8857 (tp) cc_final: 0.8589 (tt) REVERT: B 116 LEU cc_start: 0.8966 (mt) cc_final: 0.8400 (tt) REVERT: B 135 GLU cc_start: 0.8358 (pp20) cc_final: 0.8082 (pp20) REVERT: B 249 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7755 (ttpp) REVERT: C 12 LEU cc_start: 0.8121 (mt) cc_final: 0.7637 (pp) REVERT: D 12 LEU cc_start: 0.8310 (mm) cc_final: 0.7736 (pp) REVERT: D 53 SER cc_start: 0.8672 (t) cc_final: 0.8457 (t) REVERT: E 12 LEU cc_start: 0.7469 (pp) cc_final: 0.7154 (mm) REVERT: E 74 MET cc_start: 0.7283 (tmm) cc_final: 0.6564 (tmm) REVERT: E 249 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8362 (ttpp) REVERT: F 12 LEU cc_start: 0.8043 (mt) cc_final: 0.7500 (pp) REVERT: F 74 MET cc_start: 0.7904 (tmm) cc_final: 0.7389 (tmm) REVERT: F 116 LEU cc_start: 0.9061 (tp) cc_final: 0.8770 (tt) REVERT: F 231 LEU cc_start: 0.9003 (mm) cc_final: 0.8684 (mm) REVERT: G 99 LEU cc_start: 0.8917 (mt) cc_final: 0.8680 (mt) REVERT: G 273 LYS cc_start: 0.8616 (tptm) cc_final: 0.8087 (tptm) REVERT: H 12 LEU cc_start: 0.8227 (mm) cc_final: 0.7684 (pp) REVERT: H 73 GLN cc_start: 0.8057 (mt0) cc_final: 0.7536 (mp10) REVERT: H 99 LEU cc_start: 0.8747 (mt) cc_final: 0.8469 (mt) REVERT: H 237 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8311 (tm-30) REVERT: H 270 GLN cc_start: 0.7828 (tp40) cc_final: 0.7256 (tp40) REVERT: I 12 LEU cc_start: 0.8165 (mm) cc_final: 0.7605 (pp) REVERT: I 74 MET cc_start: 0.7766 (tmm) cc_final: 0.7120 (tmm) REVERT: I 78 THR cc_start: 0.7227 (p) cc_final: 0.6763 (p) REVERT: I 250 LYS cc_start: 0.8627 (tmmt) cc_final: 0.7838 (ttpt) REVERT: J 32 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7869 (tm-30) REVERT: J 74 MET cc_start: 0.7950 (tmm) cc_final: 0.7410 (tmm) REVERT: J 208 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8028 (tmmt) REVERT: K 12 LEU cc_start: 0.8163 (mt) cc_final: 0.7867 (pp) REVERT: K 32 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7745 (tm-30) REVERT: K 74 MET cc_start: 0.7716 (tmm) cc_final: 0.7170 (tmm) REVERT: K 78 THR cc_start: 0.7087 (p) cc_final: 0.6705 (p) REVERT: K 130 GLU cc_start: 0.8248 (pp20) cc_final: 0.7954 (pp20) REVERT: L 12 LEU cc_start: 0.8163 (mt) cc_final: 0.7740 (pp) REVERT: L 50 TYR cc_start: 0.8512 (m-80) cc_final: 0.8256 (m-10) REVERT: L 99 LEU cc_start: 0.8807 (mt) cc_final: 0.8539 (mt) REVERT: L 135 GLU cc_start: 0.8366 (pp20) cc_final: 0.8073 (pp20) REVERT: L 237 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8333 (tm-30) REVERT: L 249 LYS cc_start: 0.8111 (tmtt) cc_final: 0.7874 (ttpp) REVERT: M 12 LEU cc_start: 0.8064 (mt) cc_final: 0.7554 (pp) REVERT: M 74 MET cc_start: 0.7832 (tmm) cc_final: 0.7501 (tmm) REVERT: N 12 LEU cc_start: 0.8075 (mm) cc_final: 0.7569 (pp) REVERT: N 135 GLU cc_start: 0.8199 (pp20) cc_final: 0.7695 (pp20) REVERT: N 144 MET cc_start: 0.7980 (pmm) cc_final: 0.7450 (pmm) REVERT: N 249 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8115 (ttpp) REVERT: O 12 LEU cc_start: 0.8010 (mm) cc_final: 0.7610 (pp) REVERT: O 74 MET cc_start: 0.7761 (tmm) cc_final: 0.7178 (tmm) REVERT: O 128 TYR cc_start: 0.8860 (m-10) cc_final: 0.8526 (m-80) REVERT: O 233 GLU cc_start: 0.8324 (tp30) cc_final: 0.8116 (tt0) REVERT: P 12 LEU cc_start: 0.7659 (mt) cc_final: 0.7353 (pp) REVERT: P 74 MET cc_start: 0.8517 (tpp) cc_final: 0.8010 (tpp) REVERT: Q 12 LEU cc_start: 0.7849 (mp) cc_final: 0.7621 (pp) REVERT: Q 116 LEU cc_start: 0.8698 (mt) cc_final: 0.8417 (tt) REVERT: Q 130 GLU cc_start: 0.8169 (pp20) cc_final: 0.7963 (pp20) REVERT: Q 155 GLU cc_start: 0.8501 (pp20) cc_final: 0.8298 (pp20) REVERT: R 5 LEU cc_start: 0.5445 (mt) cc_final: 0.5227 (mp) REVERT: R 21 SER cc_start: 0.8861 (t) cc_final: 0.8650 (t) REVERT: R 74 MET cc_start: 0.7717 (tmm) cc_final: 0.7267 (tmm) REVERT: R 78 THR cc_start: 0.7431 (p) cc_final: 0.6858 (p) REVERT: R 99 LEU cc_start: 0.8617 (mt) cc_final: 0.8223 (mt) REVERT: R 249 LYS cc_start: 0.8396 (tttm) cc_final: 0.8035 (ttpp) REVERT: R 273 LYS cc_start: 0.8840 (mmtm) cc_final: 0.8402 (tptm) REVERT: S 53 SER cc_start: 0.8709 (t) cc_final: 0.8496 (t) REVERT: S 187 MET cc_start: 0.9363 (mmp) cc_final: 0.9114 (mmm) REVERT: S 237 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8316 (tm-30) REVERT: T 12 LEU cc_start: 0.7692 (pp) cc_final: 0.7363 (mt) REVERT: T 99 LEU cc_start: 0.8831 (mt) cc_final: 0.8591 (mt) REVERT: T 208 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8265 (tmmt) REVERT: T 249 LYS cc_start: 0.8339 (tttm) cc_final: 0.8014 (ttpp) REVERT: U 12 LEU cc_start: 0.7916 (mt) cc_final: 0.7374 (pp) REVERT: U 74 MET cc_start: 0.7844 (tmm) cc_final: 0.7577 (tmm) REVERT: U 128 TYR cc_start: 0.9036 (m-10) cc_final: 0.8701 (m-80) REVERT: U 201 LEU cc_start: 0.9398 (tp) cc_final: 0.9027 (tt) REVERT: U 249 LYS cc_start: 0.8223 (tttm) cc_final: 0.7891 (ttpp) REVERT: V 187 MET cc_start: 0.9218 (mmm) cc_final: 0.9016 (mmm) REVERT: V 249 LYS cc_start: 0.8622 (tmtt) cc_final: 0.8103 (ttpp) REVERT: V 250 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8236 (tmmt) outliers start: 2 outliers final: 0 residues processed: 878 average time/residue: 0.5738 time to fit residues: 818.4382 Evaluate side-chains 665 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 5.9990 chunk 528 optimal weight: 7.9990 chunk 481 optimal weight: 4.9990 chunk 513 optimal weight: 2.9990 chunk 309 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 403 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 464 optimal weight: 0.9980 chunk 485 optimal weight: 0.9980 chunk 511 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN H 48 ASN ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46838 Z= 0.226 Angle : 0.591 6.716 63602 Z= 0.313 Chirality : 0.041 0.199 7414 Planarity : 0.005 0.049 7898 Dihedral : 3.794 19.932 6270 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.02 % Allowed : 1.18 % Favored : 98.80 % 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: 2.73 (0.11), residues: 5786 helix: 2.83 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.48 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 118 HIS 0.005 0.001 HIS N 224 PHE 0.019 0.001 PHE Q 104 TYR 0.021 0.001 TYR I 183 ARG 0.005 0.000 ARG N 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 847 time to evaluate : 5.260 Fit side-chains REVERT: A 12 LEU cc_start: 0.7785 (pp) cc_final: 0.7549 (mt) REVERT: A 20 ASN cc_start: 0.8925 (m-40) cc_final: 0.8690 (m-40) REVERT: A 74 MET cc_start: 0.7925 (tmm) cc_final: 0.7647 (tmm) REVERT: A 78 THR cc_start: 0.7700 (p) cc_final: 0.7342 (p) REVERT: A 116 LEU cc_start: 0.8769 (tp) cc_final: 0.8458 (tt) REVERT: B 78 THR cc_start: 0.7758 (p) cc_final: 0.7472 (p) REVERT: B 249 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7813 (ttpp) REVERT: C 12 LEU cc_start: 0.8119 (mt) cc_final: 0.7641 (pp) REVERT: C 233 GLU cc_start: 0.8023 (tp30) cc_final: 0.7585 (tt0) REVERT: D 12 LEU cc_start: 0.8331 (mm) cc_final: 0.7757 (pp) REVERT: D 53 SER cc_start: 0.8704 (t) cc_final: 0.8502 (t) REVERT: E 74 MET cc_start: 0.7354 (tmm) cc_final: 0.6564 (tmm) REVERT: E 249 LYS cc_start: 0.8727 (tmtt) cc_final: 0.8181 (ttpp) REVERT: F 12 LEU cc_start: 0.8082 (mt) cc_final: 0.7539 (pp) REVERT: F 74 MET cc_start: 0.7991 (tmm) cc_final: 0.7410 (tmm) REVERT: F 116 LEU cc_start: 0.9079 (tp) cc_final: 0.8783 (tt) REVERT: F 128 TYR cc_start: 0.8904 (m-80) cc_final: 0.8485 (m-80) REVERT: F 231 LEU cc_start: 0.8985 (mm) cc_final: 0.8676 (mm) REVERT: F 271 ASP cc_start: 0.8830 (m-30) cc_final: 0.8628 (m-30) REVERT: G 99 LEU cc_start: 0.8962 (mt) cc_final: 0.8719 (mt) REVERT: G 273 LYS cc_start: 0.8609 (tptm) cc_final: 0.8051 (tptm) REVERT: H 12 LEU cc_start: 0.8249 (mm) cc_final: 0.7708 (pp) REVERT: H 99 LEU cc_start: 0.8783 (mt) cc_final: 0.8500 (mt) REVERT: H 237 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8362 (tm-30) REVERT: I 12 LEU cc_start: 0.8172 (mm) cc_final: 0.7639 (pp) REVERT: I 78 THR cc_start: 0.7198 (p) cc_final: 0.6962 (p) REVERT: I 116 LEU cc_start: 0.8899 (tp) cc_final: 0.8626 (tt) REVERT: I 242 LEU cc_start: 0.9144 (mm) cc_final: 0.8939 (mt) REVERT: I 250 LYS cc_start: 0.8647 (tmmt) cc_final: 0.7893 (ttpt) REVERT: J 32 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7768 (tm-30) REVERT: J 74 MET cc_start: 0.8064 (tmm) cc_final: 0.7555 (tmm) REVERT: J 208 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8072 (tmmt) REVERT: K 12 LEU cc_start: 0.8252 (mt) cc_final: 0.7900 (pp) REVERT: K 32 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7524 (tm-30) REVERT: K 74 MET cc_start: 0.7755 (tmm) cc_final: 0.7222 (tmm) REVERT: K 78 THR cc_start: 0.7131 (p) cc_final: 0.6744 (p) REVERT: K 130 GLU cc_start: 0.8319 (pp20) cc_final: 0.8039 (pp20) REVERT: L 12 LEU cc_start: 0.8175 (mt) cc_final: 0.7752 (pp) REVERT: L 50 TYR cc_start: 0.8529 (m-80) cc_final: 0.8316 (m-10) REVERT: L 99 LEU cc_start: 0.8845 (mt) cc_final: 0.8576 (mt) REVERT: L 249 LYS cc_start: 0.8128 (tmtt) cc_final: 0.7872 (ttpp) REVERT: M 12 LEU cc_start: 0.8100 (mt) cc_final: 0.7590 (pp) REVERT: M 74 MET cc_start: 0.7697 (tmm) cc_final: 0.7284 (tmm) REVERT: N 12 LEU cc_start: 0.8132 (mm) cc_final: 0.7625 (pp) REVERT: N 135 GLU cc_start: 0.8223 (pp20) cc_final: 0.7719 (pp20) REVERT: N 144 MET cc_start: 0.7661 (pmm) cc_final: 0.7358 (pmm) REVERT: N 249 LYS cc_start: 0.8692 (tmtt) cc_final: 0.8074 (ttpp) REVERT: O 12 LEU cc_start: 0.8043 (mm) cc_final: 0.7655 (pp) REVERT: O 74 MET cc_start: 0.7694 (tmm) cc_final: 0.7121 (tmm) REVERT: O 78 THR cc_start: 0.7641 (p) cc_final: 0.6872 (p) REVERT: O 128 TYR cc_start: 0.8897 (m-10) cc_final: 0.8546 (m-80) REVERT: P 12 LEU cc_start: 0.7716 (mt) cc_final: 0.7398 (pp) REVERT: P 74 MET cc_start: 0.8567 (tpp) cc_final: 0.8177 (tpp) REVERT: Q 116 LEU cc_start: 0.8720 (mt) cc_final: 0.8406 (tt) REVERT: Q 130 GLU cc_start: 0.8206 (pp20) cc_final: 0.7979 (pp20) REVERT: R 78 THR cc_start: 0.7375 (p) cc_final: 0.6904 (p) REVERT: R 99 LEU cc_start: 0.8677 (mt) cc_final: 0.8357 (mt) REVERT: R 233 GLU cc_start: 0.8349 (tp30) cc_final: 0.8141 (tt0) REVERT: R 242 LEU cc_start: 0.8997 (mm) cc_final: 0.8668 (mt) REVERT: R 249 LYS cc_start: 0.8450 (tttm) cc_final: 0.8071 (ttpp) REVERT: R 273 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8409 (tptm) REVERT: S 53 SER cc_start: 0.8750 (t) cc_final: 0.8537 (t) REVERT: S 187 MET cc_start: 0.9369 (mmp) cc_final: 0.9119 (mmm) REVERT: S 237 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8335 (tm-30) REVERT: T 12 LEU cc_start: 0.7751 (pp) cc_final: 0.7386 (mt) REVERT: T 99 LEU cc_start: 0.8789 (mt) cc_final: 0.8560 (mt) REVERT: T 130 GLU cc_start: 0.8353 (pp20) cc_final: 0.8086 (pp20) REVERT: T 208 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8331 (tmmt) REVERT: T 249 LYS cc_start: 0.8381 (tttm) cc_final: 0.8061 (ttpp) REVERT: U 12 LEU cc_start: 0.7943 (mt) cc_final: 0.7416 (pp) REVERT: U 74 MET cc_start: 0.7900 (tmm) cc_final: 0.7567 (tmm) REVERT: U 128 TYR cc_start: 0.9070 (m-10) cc_final: 0.8717 (m-80) REVERT: U 201 LEU cc_start: 0.9441 (tp) cc_final: 0.9071 (tt) REVERT: U 229 ARG cc_start: 0.8287 (tpt170) cc_final: 0.7903 (tpt170) REVERT: U 249 LYS cc_start: 0.8267 (tttm) cc_final: 0.7920 (ttpp) REVERT: V 187 MET cc_start: 0.9170 (mmm) cc_final: 0.8853 (mmm) REVERT: V 225 LEU cc_start: 0.8570 (mt) cc_final: 0.8238 (mt) REVERT: V 249 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8095 (ttpp) REVERT: V 250 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8272 (tmmt) outliers start: 1 outliers final: 0 residues processed: 848 average time/residue: 0.5732 time to fit residues: 788.4017 Evaluate side-chains 668 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 5.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 9.9990 chunk 543 optimal weight: 0.9980 chunk 331 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 377 optimal weight: 8.9990 chunk 569 optimal weight: 3.9990 chunk 524 optimal weight: 3.9990 chunk 453 optimal weight: 0.0030 chunk 47 optimal weight: 7.9990 chunk 350 optimal weight: 7.9990 chunk 278 optimal weight: 0.9980 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN E 44 GLN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 227 ASN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN ** V 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46838 Z= 0.195 Angle : 0.586 7.099 63602 Z= 0.309 Chirality : 0.040 0.214 7414 Planarity : 0.004 0.050 7898 Dihedral : 3.795 19.622 6270 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.11), residues: 5786 helix: 2.86 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.43 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 272 HIS 0.003 0.001 HIS V 224 PHE 0.017 0.001 PHE Q 104 TYR 0.021 0.001 TYR P 183 ARG 0.006 0.000 ARG Q 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 838 time to evaluate : 5.694 Fit side-chains REVERT: A 12 LEU cc_start: 0.7746 (pp) cc_final: 0.7527 (mt) REVERT: A 74 MET cc_start: 0.7900 (tmm) cc_final: 0.7651 (tmm) REVERT: A 78 THR cc_start: 0.7906 (p) cc_final: 0.7251 (p) REVERT: A 116 LEU cc_start: 0.8761 (tp) cc_final: 0.8444 (tt) REVERT: A 229 ARG cc_start: 0.8221 (tpt170) cc_final: 0.7811 (tpt170) REVERT: B 78 THR cc_start: 0.7652 (p) cc_final: 0.7304 (p) REVERT: B 155 GLU cc_start: 0.8397 (pp20) cc_final: 0.8175 (pp20) REVERT: B 249 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7791 (ttpp) REVERT: C 12 LEU cc_start: 0.8104 (mt) cc_final: 0.7621 (pp) REVERT: C 233 GLU cc_start: 0.7958 (tp30) cc_final: 0.7553 (tt0) REVERT: D 12 LEU cc_start: 0.8303 (mm) cc_final: 0.7739 (pp) REVERT: D 53 SER cc_start: 0.8686 (t) cc_final: 0.8473 (t) REVERT: E 74 MET cc_start: 0.7264 (tmm) cc_final: 0.6566 (tmm) REVERT: E 249 LYS cc_start: 0.8691 (tmtt) cc_final: 0.8362 (ttpp) REVERT: F 12 LEU cc_start: 0.8066 (mt) cc_final: 0.7524 (pp) REVERT: F 74 MET cc_start: 0.7940 (tmm) cc_final: 0.7386 (tmm) REVERT: F 116 LEU cc_start: 0.9037 (tp) cc_final: 0.8714 (tt) REVERT: F 128 TYR cc_start: 0.8917 (m-80) cc_final: 0.8469 (m-80) REVERT: F 231 LEU cc_start: 0.8973 (mm) cc_final: 0.8659 (mm) REVERT: F 249 LYS cc_start: 0.8579 (tmtt) cc_final: 0.7851 (ttpp) REVERT: G 74 MET cc_start: 0.8678 (tpp) cc_final: 0.8402 (tpp) REVERT: G 99 LEU cc_start: 0.8936 (mt) cc_final: 0.8688 (mt) REVERT: H 12 LEU cc_start: 0.8229 (mm) cc_final: 0.7681 (pp) REVERT: H 74 MET cc_start: 0.7608 (tmm) cc_final: 0.7004 (tmm) REVERT: H 99 LEU cc_start: 0.8748 (mt) cc_final: 0.8463 (mt) REVERT: H 176 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8135 (tm-30) REVERT: H 187 MET cc_start: 0.9354 (mmp) cc_final: 0.9122 (mmp) REVERT: H 237 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8364 (tm-30) REVERT: I 12 LEU cc_start: 0.8156 (mm) cc_final: 0.7622 (pp) REVERT: I 116 LEU cc_start: 0.8874 (tp) cc_final: 0.8581 (tt) REVERT: I 250 LYS cc_start: 0.8620 (tmmt) cc_final: 0.7870 (ttpt) REVERT: J 32 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7744 (tm-30) REVERT: J 74 MET cc_start: 0.7983 (tmm) cc_final: 0.7481 (tmm) REVERT: J 208 LYS cc_start: 0.8551 (mmmm) cc_final: 0.8052 (tmmt) REVERT: K 12 LEU cc_start: 0.8260 (mt) cc_final: 0.7905 (pp) REVERT: K 78 THR cc_start: 0.6983 (p) cc_final: 0.6576 (p) REVERT: K 130 GLU cc_start: 0.8312 (pp20) cc_final: 0.8037 (pp20) REVERT: L 12 LEU cc_start: 0.8149 (mt) cc_final: 0.7728 (pp) REVERT: L 99 LEU cc_start: 0.8793 (mt) cc_final: 0.8513 (mt) REVERT: L 135 GLU cc_start: 0.8194 (pp20) cc_final: 0.7705 (pp20) REVERT: L 237 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8239 (tm-30) REVERT: M 12 LEU cc_start: 0.8080 (mt) cc_final: 0.7554 (pp) REVERT: M 74 MET cc_start: 0.7823 (tmm) cc_final: 0.7378 (tmm) REVERT: N 12 LEU cc_start: 0.8110 (mm) cc_final: 0.7621 (pp) REVERT: N 135 GLU cc_start: 0.8208 (pp20) cc_final: 0.7759 (pp20) REVERT: N 144 MET cc_start: 0.7969 (pmm) cc_final: 0.7504 (pmm) REVERT: N 249 LYS cc_start: 0.8555 (tmtt) cc_final: 0.8029 (ttpp) REVERT: O 12 LEU cc_start: 0.7970 (mm) cc_final: 0.7590 (pp) REVERT: O 74 MET cc_start: 0.7670 (tmm) cc_final: 0.7099 (tmm) REVERT: O 78 THR cc_start: 0.7610 (p) cc_final: 0.6836 (p) REVERT: O 128 TYR cc_start: 0.8885 (m-10) cc_final: 0.8528 (m-80) REVERT: O 135 GLU cc_start: 0.8158 (pm20) cc_final: 0.7630 (pp20) REVERT: P 12 LEU cc_start: 0.7689 (mt) cc_final: 0.7380 (pp) REVERT: P 74 MET cc_start: 0.8543 (tpp) cc_final: 0.8127 (tpp) REVERT: P 78 THR cc_start: 0.8086 (p) cc_final: 0.7860 (p) REVERT: Q 116 LEU cc_start: 0.8784 (mt) cc_final: 0.8467 (tt) REVERT: Q 130 GLU cc_start: 0.8186 (pp20) cc_final: 0.7964 (pp20) REVERT: R 78 THR cc_start: 0.7362 (p) cc_final: 0.6838 (p) REVERT: R 99 LEU cc_start: 0.8657 (mt) cc_final: 0.8294 (mt) REVERT: R 233 GLU cc_start: 0.8330 (tp30) cc_final: 0.7833 (tt0) REVERT: R 249 LYS cc_start: 0.8450 (tttm) cc_final: 0.8229 (ttpp) REVERT: R 273 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8374 (tptm) REVERT: S 187 MET cc_start: 0.9359 (mmp) cc_final: 0.9106 (mmm) REVERT: T 12 LEU cc_start: 0.7718 (pp) cc_final: 0.7371 (mt) REVERT: T 99 LEU cc_start: 0.8769 (mt) cc_final: 0.8529 (mt) REVERT: T 130 GLU cc_start: 0.8355 (pp20) cc_final: 0.8120 (pp20) REVERT: T 208 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8288 (tmmt) REVERT: T 249 LYS cc_start: 0.8372 (tttm) cc_final: 0.8054 (ttpp) REVERT: U 12 LEU cc_start: 0.7916 (mt) cc_final: 0.7395 (pp) REVERT: U 74 MET cc_start: 0.7833 (tmm) cc_final: 0.7498 (tmm) REVERT: U 128 TYR cc_start: 0.9054 (m-10) cc_final: 0.8700 (m-80) REVERT: U 201 LEU cc_start: 0.9434 (tp) cc_final: 0.9074 (tt) REVERT: U 229 ARG cc_start: 0.8268 (tpt170) cc_final: 0.7862 (tpt170) REVERT: U 249 LYS cc_start: 0.8212 (tttm) cc_final: 0.7887 (ttpp) REVERT: V 187 MET cc_start: 0.9161 (mmm) cc_final: 0.8844 (mmm) REVERT: V 249 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8124 (ttpp) REVERT: V 250 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8266 (tmmt) outliers start: 0 outliers final: 0 residues processed: 838 average time/residue: 0.5643 time to fit residues: 769.7842 Evaluate side-chains 644 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 644 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 6.9990 chunk 483 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 418 optimal weight: 0.6980 chunk 67 optimal weight: 0.0050 chunk 126 optimal weight: 2.9990 chunk 454 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 466 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN U 48 ASN ** V 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107258 restraints weight = 76972.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110085 restraints weight = 43998.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111907 restraints weight = 31578.820| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46838 Z= 0.169 Angle : 0.569 7.392 63602 Z= 0.297 Chirality : 0.039 0.191 7414 Planarity : 0.004 0.048 7898 Dihedral : 3.765 18.674 6270 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.02 % Allowed : 0.47 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.11), residues: 5786 helix: 2.92 (0.08), residues: 4554 sheet: None (None), residues: 0 loop : -2.30 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 221 HIS 0.003 0.000 HIS N 224 PHE 0.017 0.001 PHE R 145 TYR 0.023 0.001 TYR I 183 ARG 0.009 0.000 ARG D 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12607.37 seconds wall clock time: 225 minutes 27.87 seconds (13527.87 seconds total)