Starting phenix.real_space_refine on Wed Feb 14 11:34:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/02_2024/6w6o_21560_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/02_2024/6w6o_21560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/02_2024/6w6o_21560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/02_2024/6w6o_21560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/02_2024/6w6o_21560_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/02_2024/6w6o_21560_neut_updated.pdb" } resolution = 3.2 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= 0.003 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 48 5.16 5 C 6244 2.51 5 N 1388 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1": "OE1" <-> "OE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1": "OE1" <-> "OE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 108": "OD1" <-> "OD2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 60": "OD1" <-> "OD2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 108": "OD1" <-> "OD2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H ARG 122": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H ARG 135": "NH1" <-> "NH2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "H GLU 194": "OE1" <-> "OE2" Residue "H PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1": "OE1" <-> "OE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9180 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "E" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "F" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "G" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "I" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.43, per 1000 atoms: 0.70 Number of scatterers: 9180 At special positions: 0 Unit cell: (150.39, 150.39, 69.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 12 15.00 O 1488 8.00 N 1388 7.00 C 6244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 17 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 24 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 17 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 24 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 17 " distance=2.03 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 24 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 31 " distance=2.03 Simple disulfide: pdb=" SG CYS I 2 " - pdb=" SG CYS I 17 " distance=2.03 Simple disulfide: pdb=" SG CYS I 9 " - pdb=" SG CYS I 24 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 31 " 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: 3.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 4 sheets defined 61.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 23 through 44 removed outlier: 3.833A pdb=" N THR A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.609A pdb=" N ASP A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 77 Processing helix chain 'A' and resid 88 through 105 removed outlier: 3.874A pdb=" N GLU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 4.283A pdb=" N VAL A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 169 removed outlier: 3.648A pdb=" N ALA A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Proline residue: A 145 - end of helix removed outlier: 5.422A pdb=" N ASN A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.766A pdb=" N THR A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 235 removed outlier: 4.215A pdb=" N TRP A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 215 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 217 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 222 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A 227 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 44 removed outlier: 3.833A pdb=" N THR D 44 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.609A pdb=" N ASP D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 77 Processing helix chain 'D' and resid 88 through 105 removed outlier: 3.874A pdb=" N GLU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 removed outlier: 4.282A pdb=" N VAL D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE D 127 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 169 removed outlier: 3.648A pdb=" N ALA D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix removed outlier: 5.422A pdb=" N ASN D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.766A pdb=" N THR D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 235 removed outlier: 4.214A pdb=" N TRP D 212 " --> pdb=" O PRO D 209 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 213 " --> pdb=" O TRP D 210 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE D 215 " --> pdb=" O TRP D 212 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 217 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 222 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 227 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 44 removed outlier: 3.832A pdb=" N THR F 44 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 removed outlier: 3.609A pdb=" N ASP F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 77 Processing helix chain 'F' and resid 88 through 105 removed outlier: 3.875A pdb=" N GLU F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 129 removed outlier: 4.283A pdb=" N VAL F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU F 124 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE F 127 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 169 removed outlier: 3.647A pdb=" N ALA F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Proline residue: F 145 - end of helix removed outlier: 5.421A pdb=" N ASN F 149 " --> pdb=" O PRO F 145 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 191 removed outlier: 3.765A pdb=" N THR F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 235 removed outlier: 4.215A pdb=" N TRP F 212 " --> pdb=" O PRO F 209 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU F 213 " --> pdb=" O TRP F 210 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE F 215 " --> pdb=" O TRP F 212 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER F 217 " --> pdb=" O TYR F 214 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY F 222 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE F 227 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 44 removed outlier: 3.832A pdb=" N THR H 44 " --> pdb=" O VAL H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 51 removed outlier: 3.609A pdb=" N ASP H 51 " --> pdb=" O ARG H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 77 Processing helix chain 'H' and resid 88 through 105 removed outlier: 3.874A pdb=" N GLU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 129 removed outlier: 4.283A pdb=" N VAL H 123 " --> pdb=" O ARG H 119 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU H 124 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA H 126 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE H 127 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 128 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 169 removed outlier: 3.648A pdb=" N ALA H 139 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Proline residue: H 145 - end of helix removed outlier: 5.421A pdb=" N ASN H 149 " --> pdb=" O PRO H 145 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 191 removed outlier: 3.766A pdb=" N THR H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 235 removed outlier: 4.215A pdb=" N TRP H 212 " --> pdb=" O PRO H 209 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 213 " --> pdb=" O TRP H 210 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE H 215 " --> pdb=" O TRP H 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER H 217 " --> pdb=" O TYR H 214 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY H 222 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE H 227 " --> pdb=" O PHE H 224 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS C 32 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 22 through 24 removed outlier: 4.136A pdb=" N LYS E 32 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS G 32 " --> pdb=" O VAL G 23 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 22 through 24 removed outlier: 4.137A pdb=" N LYS I 32 " --> pdb=" O VAL I 23 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1020 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: 2.16 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1268 1.30 - 1.42: 2532 1.42 - 1.55: 5466 1.55 - 1.68: 54 1.68 - 1.81: 72 Bond restraints: 9392 Sorted by residual: bond pdb=" C31 POV H 303 " pdb=" O31 POV H 303 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 POV A 302 " pdb=" O31 POV A 302 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C31 POV D 302 " pdb=" O31 POV D 302 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C31 POV F 303 " pdb=" O31 POV F 303 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C21 POV F 303 " pdb=" O21 POV F 303 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 9387 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.60: 204 106.60 - 113.50: 5591 113.50 - 120.40: 3446 120.40 - 127.30: 3295 127.30 - 134.20: 108 Bond angle restraints: 12644 Sorted by residual: angle pdb=" N SER D 82 " pdb=" CA SER D 82 " pdb=" CB SER D 82 " ideal model delta sigma weight residual 110.44 116.24 -5.80 1.43e+00 4.89e-01 1.64e+01 angle pdb=" N SER A 82 " pdb=" CA SER A 82 " pdb=" CB SER A 82 " ideal model delta sigma weight residual 110.44 116.21 -5.77 1.43e+00 4.89e-01 1.63e+01 angle pdb=" N SER F 82 " pdb=" CA SER F 82 " pdb=" CB SER F 82 " ideal model delta sigma weight residual 110.44 116.18 -5.74 1.43e+00 4.89e-01 1.61e+01 angle pdb=" N SER H 82 " pdb=" CA SER H 82 " pdb=" CB SER H 82 " ideal model delta sigma weight residual 110.44 116.16 -5.72 1.43e+00 4.89e-01 1.60e+01 angle pdb=" O11 POV H 301 " pdb=" P POV H 301 " pdb=" O12 POV H 301 " ideal model delta sigma weight residual 97.67 109.24 -11.57 3.00e+00 1.11e-01 1.49e+01 ... (remaining 12639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.75: 4942 28.75 - 57.49: 575 57.49 - 86.24: 131 86.24 - 114.98: 8 114.98 - 143.73: 12 Dihedral angle restraints: 5668 sinusoidal: 2580 harmonic: 3088 Sorted by residual: dihedral pdb=" CB CYS G 16 " pdb=" SG CYS G 16 " pdb=" SG CYS G 31 " pdb=" CB CYS G 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.02 69.02 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS E 16 " pdb=" SG CYS E 16 " pdb=" SG CYS E 31 " pdb=" CB CYS E 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.01 69.01 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS C 16 " pdb=" SG CYS C 16 " pdb=" SG CYS C 31 " pdb=" CB CYS C 31 " ideal model delta sinusoidal sigma weight residual -86.00 -155.01 69.01 1 1.00e+01 1.00e-02 6.16e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1019 0.048 - 0.097: 296 0.097 - 0.145: 73 0.145 - 0.193: 16 0.193 - 0.242: 20 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA TRP I 30 " pdb=" N TRP I 30 " pdb=" C TRP I 30 " pdb=" CB TRP I 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA TRP C 30 " pdb=" N TRP C 30 " pdb=" C TRP C 30 " pdb=" CB TRP C 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA TRP G 30 " pdb=" N TRP G 30 " pdb=" C TRP G 30 " pdb=" CB TRP G 30 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1421 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 81 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C LYS H 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS H 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER H 82 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 81 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C LYS F 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS F 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER F 82 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 81 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C LYS A 81 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS A 81 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 82 " -0.014 2.00e-02 2.50e+03 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 299 2.64 - 3.21: 9252 3.21 - 3.77: 13983 3.77 - 4.34: 18442 4.34 - 4.90: 30178 Nonbonded interactions: 72154 Sorted by model distance: nonbonded pdb=" O GLN E 15 " pdb=" NE2 GLN E 15 " model vdw 2.078 2.520 nonbonded pdb=" O GLN C 15 " pdb=" NE2 GLN C 15 " model vdw 2.078 2.520 nonbonded pdb=" O GLN G 15 " pdb=" NE2 GLN G 15 " model vdw 2.078 2.520 nonbonded pdb=" O GLN I 15 " pdb=" NE2 GLN I 15 " model vdw 2.079 2.520 nonbonded pdb=" N ASN G 13 " pdb=" OD1 ASN G 13 " model vdw 2.172 2.520 ... (remaining 72149 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 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.490 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.950 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.011 0.129 9392 Z= 0.665 Angle : 1.336 11.566 12644 Z= 0.605 Chirality : 0.055 0.242 1424 Planarity : 0.005 0.039 1464 Dihedral : 24.615 143.728 3608 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 53.37 Ramachandran Plot: Outliers : 1.56 % Allowed : 15.18 % Favored : 83.27 % Rotamer: Outliers : 16.39 % Allowed : 24.37 % Favored : 59.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.21), residues: 1028 helix: -2.38 (0.17), residues: 652 sheet: -4.67 (0.67), residues: 40 loop : -4.53 (0.22), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 30 HIS 0.002 0.001 HIS D 52 PHE 0.012 0.001 PHE A 215 TYR 0.010 0.002 TYR D 57 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 229 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9119 (tt) REVERT: D 184 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9136 (tt) REVERT: F 184 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9125 (tt) REVERT: H 184 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9142 (tt) outliers start: 156 outliers final: 103 residues processed: 371 average time/residue: 0.2077 time to fit residues: 105.0390 Evaluate side-chains 325 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 218 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 34 GLN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 24 CYS Chi-restraints excluded: chain E residue 34 GLN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 15 GLN Chi-restraints excluded: chain G residue 24 CYS Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 234 ILE Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 24 CYS Chi-restraints excluded: chain I residue 35 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN A 149 ASN A 179 ASN A 237 ASN C 10 ASN C 15 GLN C 34 GLN ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 149 ASN D 179 ASN D 237 ASN E 10 ASN E 15 GLN E 34 GLN ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN F 149 ASN F 179 ASN F 237 ASN G 10 ASN G 15 GLN ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 149 ASN H 179 ASN H 237 ASN I 10 ASN I 15 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9392 Z= 0.208 Angle : 0.649 6.097 12644 Z= 0.331 Chirality : 0.043 0.184 1424 Planarity : 0.004 0.025 1464 Dihedral : 22.546 146.131 1847 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 8.93 % Allowed : 24.47 % Favored : 66.60 % 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: -2.27 (0.26), residues: 1028 helix: -0.67 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -3.03 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 30 HIS 0.001 0.000 HIS A 52 PHE 0.014 0.001 PHE A 227 TYR 0.012 0.001 TYR F 214 ARG 0.002 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 250 time to evaluate : 0.993 Fit side-chains REVERT: A 110 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5636 (pp20) REVERT: C 3 LEU cc_start: 0.3977 (OUTLIER) cc_final: 0.3611 (pp) REVERT: D 110 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5537 (pp20) REVERT: D 194 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6844 (mt-10) REVERT: E 3 LEU cc_start: 0.4000 (OUTLIER) cc_final: 0.3755 (pp) REVERT: F 110 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5652 (pp20) REVERT: F 194 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6849 (mt-10) REVERT: G 3 LEU cc_start: 0.4032 (OUTLIER) cc_final: 0.3797 (pp) REVERT: H 110 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5773 (pp20) REVERT: I 3 LEU cc_start: 0.4111 (OUTLIER) cc_final: 0.3796 (pp) outliers start: 85 outliers final: 40 residues processed: 321 average time/residue: 0.1879 time to fit residues: 84.4908 Evaluate side-chains 283 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 235 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.0170 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN C 10 ASN C 34 GLN ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN E 10 ASN E 34 GLN F 22 HIS F 237 ASN G 10 ASN ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 237 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9392 Z= 0.273 Angle : 0.651 9.197 12644 Z= 0.327 Chirality : 0.043 0.202 1424 Planarity : 0.004 0.023 1464 Dihedral : 21.122 105.372 1724 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 9.66 % Allowed : 25.11 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.26), residues: 1028 helix: 0.03 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.61 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 30 HIS 0.001 0.001 HIS H 171 PHE 0.010 0.001 PHE H 205 TYR 0.007 0.001 TYR F 57 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 230 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 20 VAL cc_start: 0.6541 (OUTLIER) cc_final: 0.6316 (t) REVERT: A 110 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5704 (pp20) REVERT: C 3 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3516 (pp) REVERT: D 20 VAL cc_start: 0.6666 (OUTLIER) cc_final: 0.6446 (t) REVERT: D 110 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5758 (pp20) REVERT: E 3 LEU cc_start: 0.4051 (OUTLIER) cc_final: 0.3650 (pp) REVERT: F 20 VAL cc_start: 0.6584 (OUTLIER) cc_final: 0.6366 (t) REVERT: F 110 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5681 (pp20) REVERT: G 3 LEU cc_start: 0.4099 (OUTLIER) cc_final: 0.3659 (pp) REVERT: H 20 VAL cc_start: 0.6760 (OUTLIER) cc_final: 0.6553 (t) REVERT: H 110 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5726 (pp20) REVERT: I 3 LEU cc_start: 0.3960 (OUTLIER) cc_final: 0.3522 (pp) outliers start: 92 outliers final: 55 residues processed: 307 average time/residue: 0.1995 time to fit residues: 86.0995 Evaluate side-chains 286 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 219 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 36 ASN A 237 ASN C 10 ASN D 22 HIS D 36 ASN D 237 ASN E 10 ASN F 36 ASN F 237 ASN G 10 ASN H 22 HIS H 36 ASN I 10 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.175 Angle : 0.610 8.378 12644 Z= 0.303 Chirality : 0.041 0.206 1424 Planarity : 0.004 0.021 1464 Dihedral : 20.212 86.907 1724 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 9.24 % Allowed : 25.42 % Favored : 65.34 % 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: -0.79 (0.26), residues: 1028 helix: 0.46 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.35 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 30 HIS 0.001 0.000 HIS F 22 PHE 0.007 0.001 PHE H 215 TYR 0.008 0.001 TYR H 57 ARG 0.001 0.000 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 245 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.6689 (OUTLIER) cc_final: 0.6438 (t) REVERT: A 27 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: A 110 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5693 (pp20) REVERT: A 194 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: C 3 LEU cc_start: 0.3795 (OUTLIER) cc_final: 0.2937 (pp) REVERT: D 20 VAL cc_start: 0.6708 (OUTLIER) cc_final: 0.6470 (t) REVERT: D 27 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: D 110 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5824 (pp20) REVERT: E 3 LEU cc_start: 0.3832 (OUTLIER) cc_final: 0.2886 (pp) REVERT: F 20 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6352 (t) REVERT: F 27 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: F 110 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5696 (pp20) REVERT: G 3 LEU cc_start: 0.3957 (OUTLIER) cc_final: 0.3593 (pp) REVERT: H 20 VAL cc_start: 0.6676 (OUTLIER) cc_final: 0.6461 (t) REVERT: H 27 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: H 110 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5737 (pp20) REVERT: H 194 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: I 3 LEU cc_start: 0.3707 (OUTLIER) cc_final: 0.3360 (pp) outliers start: 88 outliers final: 50 residues processed: 312 average time/residue: 0.1870 time to fit residues: 82.2296 Evaluate side-chains 294 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 226 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN C 10 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9392 Z= 0.220 Angle : 0.635 9.368 12644 Z= 0.312 Chirality : 0.042 0.173 1424 Planarity : 0.004 0.020 1464 Dihedral : 20.059 91.403 1716 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 8.82 % Allowed : 27.73 % Favored : 63.45 % 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: -0.62 (0.26), residues: 1028 helix: 0.44 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.12 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 30 HIS 0.001 0.000 HIS D 171 PHE 0.022 0.001 PHE D 105 TYR 0.015 0.001 TYR H 57 ARG 0.002 0.000 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 228 time to evaluate : 1.007 Fit side-chains REVERT: A 27 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: A 110 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5726 (pp20) REVERT: A 194 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: D 20 VAL cc_start: 0.6608 (OUTLIER) cc_final: 0.6404 (t) REVERT: D 110 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5802 (pp20) REVERT: F 20 VAL cc_start: 0.6591 (OUTLIER) cc_final: 0.6385 (t) REVERT: F 27 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: F 110 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5736 (pp20) REVERT: G 3 LEU cc_start: 0.3756 (OUTLIER) cc_final: 0.3355 (pp) REVERT: H 20 VAL cc_start: 0.6619 (OUTLIER) cc_final: 0.6409 (t) REVERT: H 27 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: H 110 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5762 (pp20) REVERT: H 194 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: I 3 LEU cc_start: 0.3653 (OUTLIER) cc_final: 0.3300 (pp) outliers start: 84 outliers final: 48 residues processed: 292 average time/residue: 0.1902 time to fit residues: 77.9703 Evaluate side-chains 283 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 221 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 ASN Chi-restraints excluded: chain I residue 16 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 237 ASN C 10 ASN D 36 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN F 36 ASN F 237 ASN G 10 ASN H 36 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9392 Z= 0.180 Angle : 0.647 9.458 12644 Z= 0.312 Chirality : 0.041 0.149 1424 Planarity : 0.003 0.020 1464 Dihedral : 19.364 95.495 1706 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 7.67 % Allowed : 29.94 % Favored : 62.39 % 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: -0.38 (0.26), residues: 1028 helix: 0.62 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 30 HIS 0.001 0.000 HIS A 22 PHE 0.029 0.001 PHE F 105 TYR 0.020 0.001 TYR A 57 ARG 0.002 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 228 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 27 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: A 110 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5710 (pp20) REVERT: A 194 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6843 (tt0) REVERT: D 20 VAL cc_start: 0.6651 (OUTLIER) cc_final: 0.6430 (t) REVERT: D 49 TYR cc_start: 0.7674 (t80) cc_final: 0.6758 (t80) REVERT: D 110 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5681 (pp20) REVERT: F 20 VAL cc_start: 0.6578 (OUTLIER) cc_final: 0.6372 (t) REVERT: F 27 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: F 49 TYR cc_start: 0.7673 (t80) cc_final: 0.6719 (t80) REVERT: F 110 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5733 (pp20) REVERT: H 27 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: H 49 TYR cc_start: 0.7693 (t80) cc_final: 0.6715 (t80) REVERT: H 110 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5696 (pp20) REVERT: H 194 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6862 (tt0) outliers start: 73 outliers final: 43 residues processed: 285 average time/residue: 0.2011 time to fit residues: 80.8426 Evaluate side-chains 267 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 213 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 0.0010 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN D 237 ASN E 10 ASN F 237 ASN G 10 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9392 Z= 0.165 Angle : 0.652 10.279 12644 Z= 0.310 Chirality : 0.040 0.140 1424 Planarity : 0.003 0.020 1464 Dihedral : 18.550 100.881 1684 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 7.04 % Allowed : 30.67 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1028 helix: 0.67 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 30 HIS 0.001 0.000 HIS A 22 PHE 0.026 0.001 PHE F 105 TYR 0.019 0.001 TYR F 57 ARG 0.002 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 227 time to evaluate : 1.085 Fit side-chains REVERT: A 81 LYS cc_start: 0.4189 (OUTLIER) cc_final: 0.3620 (tppt) REVERT: A 110 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.5646 (pp20) REVERT: D 20 VAL cc_start: 0.6463 (OUTLIER) cc_final: 0.6262 (t) REVERT: D 81 LYS cc_start: 0.4375 (OUTLIER) cc_final: 0.3837 (tppt) REVERT: D 110 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5652 (pp20) REVERT: F 65 TRP cc_start: 0.7326 (OUTLIER) cc_final: 0.6845 (t-100) REVERT: F 81 LYS cc_start: 0.4526 (OUTLIER) cc_final: 0.3941 (tppt) REVERT: F 110 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5602 (pp20) REVERT: F 202 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8312 (mmt180) REVERT: H 27 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: H 65 TRP cc_start: 0.7232 (OUTLIER) cc_final: 0.6873 (t-100) REVERT: H 81 LYS cc_start: 0.4259 (OUTLIER) cc_final: 0.3714 (tppt) REVERT: H 110 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5665 (pp20) outliers start: 67 outliers final: 39 residues processed: 271 average time/residue: 0.1912 time to fit residues: 73.0907 Evaluate side-chains 262 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 210 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 237 ASN C 10 ASN D 36 ASN D 237 ASN E 10 ASN F 17 GLN F 36 ASN F 237 ASN H 36 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.197 Angle : 0.667 10.091 12644 Z= 0.317 Chirality : 0.041 0.132 1424 Planarity : 0.003 0.019 1464 Dihedral : 18.561 101.409 1680 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.41 % Allowed : 30.78 % Favored : 62.82 % 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: -0.23 (0.26), residues: 1028 helix: 0.71 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.93 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 196 HIS 0.001 0.000 HIS A 22 PHE 0.023 0.001 PHE F 105 TYR 0.017 0.001 TYR A 57 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 219 time to evaluate : 1.058 Fit side-chains REVERT: A 27 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7477 (m-80) REVERT: A 81 LYS cc_start: 0.4535 (OUTLIER) cc_final: 0.3927 (tppt) REVERT: A 110 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5703 (pp20) REVERT: D 81 LYS cc_start: 0.4432 (OUTLIER) cc_final: 0.3848 (tppt) REVERT: D 110 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5706 (pp20) REVERT: F 81 LYS cc_start: 0.4582 (OUTLIER) cc_final: 0.3983 (tppt) REVERT: F 110 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5754 (pp20) REVERT: F 202 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8301 (mmt180) REVERT: H 27 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: H 81 LYS cc_start: 0.4477 (OUTLIER) cc_final: 0.3869 (tppt) REVERT: H 110 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5754 (pp20) outliers start: 61 outliers final: 39 residues processed: 261 average time/residue: 0.1788 time to fit residues: 66.9384 Evaluate side-chains 260 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 36 ASN A 237 ASN C 10 ASN D 36 ASN D 237 ASN E 10 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN H 36 ASN H 237 ASN I 10 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9392 Z= 0.190 Angle : 0.706 10.780 12644 Z= 0.329 Chirality : 0.041 0.159 1424 Planarity : 0.004 0.020 1464 Dihedral : 18.340 106.888 1678 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.88 % Allowed : 31.51 % Favored : 62.61 % 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: -0.22 (0.26), residues: 1028 helix: 0.69 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.87 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 196 HIS 0.002 0.000 HIS H 22 PHE 0.032 0.001 PHE H 105 TYR 0.016 0.001 TYR H 57 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 213 time to evaluate : 0.978 Fit side-chains REVERT: A 27 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: A 65 TRP cc_start: 0.7201 (OUTLIER) cc_final: 0.6854 (t-100) REVERT: A 81 LYS cc_start: 0.4485 (OUTLIER) cc_final: 0.3942 (tppt) REVERT: A 110 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5736 (pp20) REVERT: D 65 TRP cc_start: 0.7266 (OUTLIER) cc_final: 0.6856 (t-100) REVERT: D 81 LYS cc_start: 0.4363 (OUTLIER) cc_final: 0.3834 (tppt) REVERT: D 110 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5653 (pp20) REVERT: F 27 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: F 65 TRP cc_start: 0.7231 (OUTLIER) cc_final: 0.6834 (t-100) REVERT: F 81 LYS cc_start: 0.4524 (OUTLIER) cc_final: 0.3984 (tppt) REVERT: F 110 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.5744 (pp20) REVERT: F 202 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8318 (mmt180) REVERT: H 27 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: H 65 TRP cc_start: 0.7176 (OUTLIER) cc_final: 0.6890 (t-100) REVERT: H 81 LYS cc_start: 0.4309 (OUTLIER) cc_final: 0.3756 (tppt) REVERT: H 110 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5685 (pp20) outliers start: 56 outliers final: 35 residues processed: 249 average time/residue: 0.1744 time to fit residues: 62.6671 Evaluate side-chains 256 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 134 ARG Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 63 optimal weight: 0.4980 chunk 84 optimal weight: 0.3980 chunk 24 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN C 10 ASN D 36 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9392 Z= 0.184 Angle : 0.724 10.823 12644 Z= 0.335 Chirality : 0.042 0.169 1424 Planarity : 0.004 0.022 1464 Dihedral : 17.987 111.672 1678 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.78 % Allowed : 32.14 % Favored : 62.08 % 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: -0.22 (0.26), residues: 1028 helix: 0.67 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.81 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 196 HIS 0.002 0.001 HIS F 22 PHE 0.032 0.001 PHE F 105 TYR 0.013 0.001 TYR H 57 ARG 0.003 0.000 ARG C 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 211 time to evaluate : 0.992 Fit side-chains REVERT: A 65 TRP cc_start: 0.7208 (m-10) cc_final: 0.6861 (t-100) REVERT: A 81 LYS cc_start: 0.4336 (OUTLIER) cc_final: 0.3826 (tppt) REVERT: A 110 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5719 (pp20) REVERT: D 49 TYR cc_start: 0.7575 (t80) cc_final: 0.6624 (t80) REVERT: D 65 TRP cc_start: 0.7181 (OUTLIER) cc_final: 0.6808 (t-100) REVERT: D 81 LYS cc_start: 0.4348 (OUTLIER) cc_final: 0.3962 (tppt) REVERT: D 110 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5719 (pp20) REVERT: F 27 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: F 65 TRP cc_start: 0.7153 (OUTLIER) cc_final: 0.6783 (t-100) REVERT: F 81 LYS cc_start: 0.4416 (OUTLIER) cc_final: 0.3983 (tppt) REVERT: F 110 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5756 (pp20) REVERT: F 202 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8351 (mmt180) REVERT: H 27 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: H 65 TRP cc_start: 0.7193 (OUTLIER) cc_final: 0.6881 (t-100) REVERT: H 81 LYS cc_start: 0.4182 (OUTLIER) cc_final: 0.3768 (tppt) REVERT: H 110 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5641 (pp20) outliers start: 55 outliers final: 32 residues processed: 245 average time/residue: 0.1878 time to fit residues: 65.0992 Evaluate side-chains 250 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 65 TRP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain I residue 13 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN D 36 ASN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN F 36 ASN ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN ** H 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.158803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106745 restraints weight = 13077.459| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.11 r_work: 0.3157 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9392 Z= 0.279 Angle : 0.758 11.514 12644 Z= 0.356 Chirality : 0.044 0.311 1424 Planarity : 0.004 0.027 1464 Dihedral : 18.926 117.083 1678 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.46 % Allowed : 32.67 % Favored : 61.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1028 helix: 0.63 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 196 HIS 0.001 0.001 HIS F 22 PHE 0.031 0.002 PHE F 105 TYR 0.016 0.002 TYR F 57 ARG 0.002 0.000 ARG C 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.21 seconds wall clock time: 42 minutes 40.25 seconds (2560.25 seconds total)