Starting phenix.real_space_refine (version: dev) on Mon Dec 12 05:38:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/12_2022/6w6o_21560_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/12_2022/6w6o_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_21560/12_2022/6w6o_21560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/12_2022/6w6o_21560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/12_2022/6w6o_21560_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6o_21560/12_2022/6w6o_21560_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 Convert atoms to be neutral 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-4807/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: 5.60, per 1000 atoms: 0.61 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: 3.75 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: 0.51 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: 2.12 Time building geometry restraints manager: 3.96 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: 4898 28.75 - 57.49: 554 57.49 - 86.24: 124 86.24 - 114.98: 8 114.98 - 143.73: 12 Dihedral angle restraints: 5596 sinusoidal: 2508 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 5593 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 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. 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.740 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 25.890 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 24.383 143.728 3536 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 % 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 *********************** 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 : 1.143 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 outliers start: 156 outliers final: 103 residues processed: 371 average time/residue: 0.2056 time to fit residues: 103.9815 Evaluate side-chains 321 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 218 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.1132 time to fit residues: 20.2616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ** 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 ** 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9392 Z= 0.199 Angle : 0.700 10.283 12644 Z= 0.349 Chirality : 0.044 0.183 1424 Planarity : 0.004 0.023 1464 Dihedral : 21.058 145.222 1568 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 4.20 % 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: -2.26 (0.26), residues: 1028 helix: -0.66 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -3.02 (0.31), residues: 364 *********************** 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 288 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 248 time to evaluate : 1.001 Fit side-chains outliers start: 40 outliers final: 20 residues processed: 284 average time/residue: 0.1807 time to fit residues: 73.9512 Evaluate side-chains 253 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1900 time to fit residues: 6.6372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.2980 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 0.0170 chunk 89 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN E 10 ASN F 22 HIS F 237 ASN G 10 ASN ** H 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 237 ASN I 10 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9392 Z= 0.174 Angle : 0.632 9.018 12644 Z= 0.314 Chirality : 0.042 0.192 1424 Planarity : 0.004 0.021 1464 Dihedral : 18.799 96.027 1568 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 4.83 % 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: -1.21 (0.26), residues: 1028 helix: 0.15 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 368 *********************** 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 300 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 254 time to evaluate : 1.105 Fit side-chains outliers start: 46 outliers final: 21 residues processed: 288 average time/residue: 0.1622 time to fit residues: 68.8575 Evaluate side-chains 247 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 226 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0892 time to fit residues: 4.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 C 10 ASN D 22 HIS D 36 ASN E 10 ASN F 36 ASN G 10 ASN H 22 HIS H 36 ASN I 10 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3792 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= 0.183 Angle : 0.621 8.519 12644 Z= 0.308 Chirality : 0.041 0.195 1424 Planarity : 0.003 0.022 1464 Dihedral : 18.591 88.622 1568 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 3.36 % 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: -0.78 (0.26), residues: 1028 helix: 0.49 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.41 (0.29), residues: 368 *********************** 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 268 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 1.091 Fit side-chains outliers start: 32 outliers final: 6 residues processed: 251 average time/residue: 0.1644 time to fit residues: 61.1029 Evaluate side-chains 230 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 224 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0875 time to fit residues: 2.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN C 34 GLN E 10 ASN G 10 ASN I 10 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3877 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= 0.269 Angle : 0.642 8.562 12644 Z= 0.320 Chirality : 0.042 0.201 1424 Planarity : 0.004 0.020 1464 Dihedral : 18.943 93.001 1568 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 4.20 % 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: -0.61 (0.26), residues: 1028 helix: 0.63 (0.21), residues: 660 sheet: None (None), residues: 0 loop : -2.38 (0.28), residues: 368 *********************** 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 278 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 238 time to evaluate : 0.998 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 267 average time/residue: 0.1673 time to fit residues: 65.8006 Evaluate side-chains 235 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0845 time to fit residues: 3.5805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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 ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 10 ASN F 36 ASN G 10 ASN G 15 GLN H 36 ASN I 10 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9392 Z= 0.177 Angle : 0.633 9.194 12644 Z= 0.312 Chirality : 0.041 0.174 1424 Planarity : 0.003 0.021 1464 Dihedral : 18.093 98.475 1568 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 2.42 % 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: -0.37 (0.26), residues: 1028 helix: 0.68 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.14 (0.31), residues: 344 *********************** 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 248 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 1.187 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 241 average time/residue: 0.1662 time to fit residues: 58.8840 Evaluate side-chains 219 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0830 time to fit residues: 3.0633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN C 34 GLN 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: 0.7326 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9392 Z= 0.213 Angle : 0.660 9.343 12644 Z= 0.321 Chirality : 0.042 0.158 1424 Planarity : 0.004 0.020 1464 Dihedral : 17.989 99.347 1568 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 1.37 % 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: -0.33 (0.26), residues: 1028 helix: 0.68 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 344 *********************** 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 236 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 223 time to evaluate : 1.084 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 225 average time/residue: 0.1680 time to fit residues: 56.0510 Evaluate side-chains 214 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 208 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0864 time to fit residues: 2.3877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 36 ASN G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9392 Z= 0.236 Angle : 0.700 11.613 12644 Z= 0.335 Chirality : 0.042 0.160 1424 Planarity : 0.004 0.020 1464 Dihedral : 17.912 104.281 1568 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1028 helix: 0.51 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 328 *********************** 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 235 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 220 time to evaluate : 1.166 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 223 average time/residue: 0.1611 time to fit residues: 54.0363 Evaluate side-chains 213 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 209 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0846 time to fit residues: 2.0690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 E 10 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9392 Z= 0.187 Angle : 0.702 12.997 12644 Z= 0.332 Chirality : 0.042 0.148 1424 Planarity : 0.004 0.023 1464 Dihedral : 17.195 108.204 1568 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.47 % 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: 0.72 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 344 *********************** 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 220 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 1.060 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 211 average time/residue: 0.1699 time to fit residues: 52.9869 Evaluate side-chains 200 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 196 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0842 time to fit residues: 2.0673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 E 10 ASN F 36 ASN G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9392 Z= 0.236 Angle : 0.751 13.422 12644 Z= 0.350 Chirality : 0.045 0.334 1424 Planarity : 0.004 0.027 1464 Dihedral : 17.482 108.581 1568 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.84 % 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: -0.40 (0.26), residues: 1028 helix: 0.53 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.95 (0.32), residues: 328 ********************** 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 219 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 0.999 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 213 average time/residue: 0.1641 time to fit residues: 52.2138 Evaluate side-chains 204 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1021 time to fit residues: 1.8435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN H 36 ASN I 10 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.163037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112921 restraints weight = 13306.999| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.13 r_work: 0.3262 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4900 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 : 0.743 13.502 12644 Z= 0.340 Chirality : 0.044 0.330 1424 Planarity : 0.004 0.030 1464 Dihedral : 16.676 118.127 1568 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 0.53 % 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: -0.25 (0.27), residues: 1028 helix: 0.59 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 328 =============================================================================== Job complete usr+sys time: 2145.05 seconds wall clock time: 39 minutes 22.54 seconds (2362.54 seconds total)