Starting phenix.real_space_refine on Fri Feb 16 00:01:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/02_2024/7dlu_30713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/02_2024/7dlu_30713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/02_2024/7dlu_30713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/02_2024/7dlu_30713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/02_2024/7dlu_30713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/02_2024/7dlu_30713.pdb" } resolution = 2.5 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= -0.005 sd= 0.171 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 8911 2.51 5 N 2345 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ASP 253": "OD1" <-> "OD2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 58": "NH1" <-> "NH2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 129": "OD1" <-> "OD2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "F GLU 258": "OE1" <-> "OE2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ARG 58": "NH1" <-> "NH2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 129": "OD1" <-> "OD2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "G ASP 253": "OD1" <-> "OD2" Residue "G GLU 258": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13727 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1961 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "B" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1961 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "C" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1961 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "D" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1961 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "E" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1961 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "F" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1961 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain: "G" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1961 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Time building chain proxies: 6.78, per 1000 atoms: 0.49 Number of scatterers: 13727 At special positions: 0 Unit cell: (101.091, 100.004, 141.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 2443 8.00 N 2345 7.00 C 8911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.17 Conformation dependent library (CDL) restraints added in 2.6 seconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 54.2% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL A 19 " --> pdb=" O TRP A 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 removed outlier: 3.510A pdb=" N GLY A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 105 Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'B' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL B 19 " --> pdb=" O TRP B 15 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 85 removed outlier: 3.510A pdb=" N GLY B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 105 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 239 through 256 removed outlier: 4.751A pdb=" N ARG B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'C' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL C 19 " --> pdb=" O TRP C 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 25 " --> pdb=" O GLU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 85 removed outlier: 3.511A pdb=" N GLY C 62 " --> pdb=" O ARG C 58 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 105 Processing helix chain 'C' and resid 106 through 122 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'D' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL D 19 " --> pdb=" O TRP D 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 85 removed outlier: 3.511A pdb=" N GLY D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 105 Processing helix chain 'D' and resid 106 through 122 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 239 through 256 removed outlier: 4.751A pdb=" N ARG D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'E' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL E 19 " --> pdb=" O TRP E 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 85 removed outlier: 3.511A pdb=" N GLY E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE E 63 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E 67 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 105 Processing helix chain 'E' and resid 106 through 122 Processing helix chain 'E' and resid 162 through 167 Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG E 252 " --> pdb=" O ASN E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'F' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL F 19 " --> pdb=" O TRP F 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 85 removed outlier: 3.510A pdb=" N GLY F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 67 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 105 Processing helix chain 'F' and resid 106 through 122 Processing helix chain 'F' and resid 162 through 167 Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 259 No H-bonds generated for 'chain 'F' and resid 257 through 259' Processing helix chain 'G' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL G 19 " --> pdb=" O TRP G 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 25 " --> pdb=" O GLU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 85 removed outlier: 3.511A pdb=" N GLY G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 67 " --> pdb=" O PHE G 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 105 Processing helix chain 'G' and resid 106 through 122 Processing helix chain 'G' and resid 162 through 167 Processing helix chain 'G' and resid 192 through 202 Processing helix chain 'G' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG G 252 " --> pdb=" O ASN G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 259 No H-bonds generated for 'chain 'G' and resid 257 through 259' Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133 removed outlier: 6.798A pdb=" N VAL A 149 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 143 " --> pdb=" O HIS A 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 149 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 143 " --> pdb=" O HIS B 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 149 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE C 143 " --> pdb=" O HIS C 147 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 149 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE D 143 " --> pdb=" O HIS D 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS D 147 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E 149 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE E 143 " --> pdb=" O HIS E 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL F 149 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE F 143 " --> pdb=" O HIS F 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS F 147 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL G 149 " --> pdb=" O ASP G 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE G 143 " --> pdb=" O HIS G 147 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS G 147 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR A 228 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 272 removed outlier: 6.827A pdb=" N ARG A 267 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL B 272 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 269 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG B 267 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL C 272 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 269 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG C 267 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL D 272 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL C 269 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG D 267 " --> pdb=" O LYS E 270 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL E 272 " --> pdb=" O ARG D 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 269 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG E 267 " --> pdb=" O LYS F 270 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL F 272 " --> pdb=" O ARG E 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL E 269 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG F 267 " --> pdb=" O LYS G 270 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL G 272 " --> pdb=" O ARG F 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL F 269 " --> pdb=" O VAL G 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AA6, first strand: chain 'B' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR B 228 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.613A pdb=" N THR C 228 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR D 228 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 178 through 181 Processing sheet with id=AB3, first strand: chain 'E' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR E 228 " --> pdb=" O SER E 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AB5, first strand: chain 'F' and resid 178 through 181 removed outlier: 4.613A pdb=" N THR F 228 " --> pdb=" O SER F 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 178 through 181 Processing sheet with id=AB7, first strand: chain 'G' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR G 228 " --> pdb=" O SER G 220 " (cutoff:3.500A) 957 hydrogen bonds defined for protein. 2745 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: 4.09 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4422 1.34 - 1.46: 1847 1.46 - 1.57: 7647 1.57 - 1.69: 0 1.69 - 1.80: 56 Bond restraints: 13972 Sorted by residual: bond pdb=" C GLU F 249 " pdb=" O GLU F 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.42e+00 bond pdb=" C GLU B 249 " pdb=" O GLU B 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.41e+00 bond pdb=" C GLU E 249 " pdb=" O GLU E 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.38e+00 bond pdb=" C GLU D 249 " pdb=" O GLU D 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.38e+00 bond pdb=" C GLU A 249 " pdb=" O GLU A 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.38e+00 ... (remaining 13967 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.26: 388 107.26 - 113.95: 8255 113.95 - 120.65: 5661 120.65 - 127.35: 4582 127.35 - 134.04: 147 Bond angle restraints: 19033 Sorted by residual: angle pdb=" C VAL C 181 " pdb=" N ILE C 182 " pdb=" CA ILE C 182 " ideal model delta sigma weight residual 121.97 112.47 9.50 1.80e+00 3.09e-01 2.79e+01 angle pdb=" C VAL F 181 " pdb=" N ILE F 182 " pdb=" CA ILE F 182 " ideal model delta sigma weight residual 121.97 112.47 9.50 1.80e+00 3.09e-01 2.79e+01 angle pdb=" C VAL E 181 " pdb=" N ILE E 182 " pdb=" CA ILE E 182 " ideal model delta sigma weight residual 121.97 112.48 9.49 1.80e+00 3.09e-01 2.78e+01 angle pdb=" C VAL G 181 " pdb=" N ILE G 182 " pdb=" CA ILE G 182 " ideal model delta sigma weight residual 121.97 112.48 9.49 1.80e+00 3.09e-01 2.78e+01 angle pdb=" C VAL A 181 " pdb=" N ILE A 182 " pdb=" CA ILE A 182 " ideal model delta sigma weight residual 121.97 112.48 9.49 1.80e+00 3.09e-01 2.78e+01 ... (remaining 19028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 6732 11.72 - 23.45: 920 23.45 - 35.17: 342 35.17 - 46.90: 161 46.90 - 58.62: 70 Dihedral angle restraints: 8225 sinusoidal: 3094 harmonic: 5131 Sorted by residual: dihedral pdb=" CA ASP G 212 " pdb=" C ASP G 212 " pdb=" N PRO G 213 " pdb=" CA PRO G 213 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP E 212 " pdb=" C ASP E 212 " pdb=" N PRO E 213 " pdb=" CA PRO E 213 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP F 212 " pdb=" C ASP F 212 " pdb=" N PRO F 213 " pdb=" CA PRO F 213 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 8222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1284 0.031 - 0.063: 651 0.063 - 0.094: 231 0.094 - 0.125: 137 0.125 - 0.156: 21 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA VAL G 181 " pdb=" N VAL G 181 " pdb=" C VAL G 181 " pdb=" CB VAL G 181 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA VAL C 181 " pdb=" N VAL C 181 " pdb=" C VAL C 181 " pdb=" CB VAL C 181 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA VAL B 181 " pdb=" N VAL B 181 " pdb=" C VAL B 181 " pdb=" CB VAL B 181 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2321 not shown) Planarity restraints: 2380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 264 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO B 265 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 264 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO E 265 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO E 265 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 265 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 264 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO C 265 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.040 5.00e-02 4.00e+02 ... (remaining 2377 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 14 2.28 - 2.94: 5922 2.94 - 3.59: 19242 3.59 - 4.25: 30076 4.25 - 4.90: 52046 Nonbonded interactions: 107300 Sorted by model distance: nonbonded pdb=" OD2 ASP A 154 " pdb=" NH2 ARG B 179 " model vdw 1.627 2.520 nonbonded pdb=" OD2 ASP C 154 " pdb=" NH2 ARG D 179 " model vdw 1.627 2.520 nonbonded pdb=" OD2 ASP E 154 " pdb=" NH2 ARG F 179 " model vdw 1.627 2.520 nonbonded pdb=" OD2 ASP B 154 " pdb=" NH2 ARG C 179 " model vdw 1.627 2.520 nonbonded pdb=" NH2 ARG A 179 " pdb=" OD2 ASP G 154 " model vdw 1.627 2.520 ... (remaining 107295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.600 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: 3.730 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.050 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.004 0.024 13972 Z= 0.283 Angle : 0.717 9.502 19033 Z= 0.409 Chirality : 0.047 0.156 2324 Planarity : 0.005 0.072 2380 Dihedral : 15.055 58.623 4935 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.59 % Favored : 92.64 % Rotamer: Outliers : 6.73 % Allowed : 16.35 % Favored : 76.92 % 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: -1.31 (0.19), residues: 1806 helix: 0.20 (0.16), residues: 938 sheet: -2.35 (0.26), residues: 273 loop : -1.67 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 130 HIS 0.001 0.000 HIS D 147 PHE 0.021 0.002 PHE E 63 TYR 0.005 0.001 TYR E 173 ARG 0.009 0.001 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 217 time to evaluate : 1.634 Fit side-chains REVERT: A 46 ARG cc_start: 0.6345 (ttm170) cc_final: 0.5881 (ttt90) REVERT: A 87 GLN cc_start: 0.8645 (mm110) cc_final: 0.8092 (mm-40) REVERT: A 145 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7616 (pp) REVERT: B 46 ARG cc_start: 0.6089 (ttm170) cc_final: 0.5405 (ttt90) REVERT: B 145 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7594 (pp) REVERT: B 270 LYS cc_start: 0.8943 (tttt) cc_final: 0.8722 (tttt) REVERT: C 46 ARG cc_start: 0.6610 (ttm170) cc_final: 0.5959 (ttt90) REVERT: C 51 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7148 (mp) REVERT: C 145 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7436 (pp) REVERT: C 180 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8410 (ttt180) REVERT: C 270 LYS cc_start: 0.8921 (tttt) cc_final: 0.8672 (tttm) REVERT: D 46 ARG cc_start: 0.6415 (ttm170) cc_final: 0.5716 (ttt-90) REVERT: D 95 ILE cc_start: 0.8017 (mp) cc_final: 0.7678 (mt) REVERT: D 126 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8567 (pttt) REVERT: D 145 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7563 (pp) REVERT: E 46 ARG cc_start: 0.6440 (ttm170) cc_final: 0.5685 (ttt90) REVERT: E 51 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7014 (mp) REVERT: E 145 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7341 (pp) REVERT: F 46 ARG cc_start: 0.6336 (ttm170) cc_final: 0.5661 (ttt90) REVERT: F 54 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6829 (mtt-85) REVERT: F 87 GLN cc_start: 0.8736 (mm110) cc_final: 0.8268 (mm-40) REVERT: F 126 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8541 (pttt) REVERT: F 141 ASP cc_start: 0.8054 (t0) cc_final: 0.7816 (t70) REVERT: F 145 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7424 (pp) REVERT: G 46 ARG cc_start: 0.6425 (ttm170) cc_final: 0.5765 (ttt-90) REVERT: G 51 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7337 (mp) REVERT: G 145 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7511 (pp) REVERT: G 270 LYS cc_start: 0.8883 (tttt) cc_final: 0.8461 (tttp) outliers start: 98 outliers final: 53 residues processed: 306 average time/residue: 1.3245 time to fit residues: 439.9224 Evaluate side-chains 253 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 189 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 87 GLN A 147 HIS A 155 ASN A 248 ASN B 61 GLN B 147 HIS B 155 ASN B 248 ASN C 61 GLN C 147 HIS C 155 ASN C 248 ASN D 61 GLN D 147 HIS D 155 ASN D 248 ASN E 61 GLN E 147 HIS E 155 ASN E 197 GLN E 248 ASN F 61 GLN F 87 GLN F 147 HIS F 155 ASN F 248 ASN G 61 GLN G 147 HIS G 155 ASN G 248 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13972 Z= 0.189 Angle : 0.629 8.953 19033 Z= 0.337 Chirality : 0.045 0.138 2324 Planarity : 0.005 0.068 2380 Dihedral : 8.451 58.545 2045 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.87 % Favored : 93.36 % Rotamer: Outliers : 3.37 % Allowed : 22.12 % Favored : 74.52 % 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: 0.07 (0.20), residues: 1806 helix: 1.38 (0.17), residues: 938 sheet: -1.85 (0.27), residues: 273 loop : -1.07 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 15 HIS 0.001 0.001 HIS C 147 PHE 0.012 0.001 PHE C 63 TYR 0.009 0.001 TYR E 173 ARG 0.003 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 1.604 Fit side-chains REVERT: A 46 ARG cc_start: 0.6383 (ttm170) cc_final: 0.5840 (ttt90) REVERT: A 87 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8137 (mm-40) REVERT: A 145 ILE cc_start: 0.7621 (mt) cc_final: 0.7367 (pp) REVERT: A 232 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7911 (mtt-85) REVERT: B 46 ARG cc_start: 0.6071 (ttm170) cc_final: 0.5346 (ttt90) REVERT: B 145 ILE cc_start: 0.7754 (mt) cc_final: 0.7486 (pp) REVERT: B 232 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7797 (mtt-85) REVERT: B 250 LYS cc_start: 0.6796 (mtmt) cc_final: 0.6553 (mtmm) REVERT: B 270 LYS cc_start: 0.8891 (tttt) cc_final: 0.8665 (tttt) REVERT: C 46 ARG cc_start: 0.6569 (ttm170) cc_final: 0.5834 (ttt90) REVERT: C 145 ILE cc_start: 0.7595 (mt) cc_final: 0.7177 (pp) REVERT: C 232 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7930 (mtt-85) REVERT: C 270 LYS cc_start: 0.8892 (tttt) cc_final: 0.8500 (tttp) REVERT: D 46 ARG cc_start: 0.6347 (ttm170) cc_final: 0.5589 (ttp80) REVERT: D 51 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7539 (mp) REVERT: D 95 ILE cc_start: 0.7939 (mp) cc_final: 0.7580 (mt) REVERT: D 126 LYS cc_start: 0.8778 (ptpp) cc_final: 0.8539 (pttt) REVERT: D 145 ILE cc_start: 0.7709 (mt) cc_final: 0.7387 (pp) REVERT: D 232 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7926 (mtt-85) REVERT: E 46 ARG cc_start: 0.6248 (ttm170) cc_final: 0.5524 (ttt90) REVERT: E 145 ILE cc_start: 0.7797 (mt) cc_final: 0.7371 (pp) REVERT: E 154 ASP cc_start: 0.6961 (t70) cc_final: 0.6640 (t0) REVERT: E 232 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7809 (mtt-85) REVERT: F 46 ARG cc_start: 0.6383 (ttm170) cc_final: 0.5979 (mtp-110) REVERT: F 51 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7108 (mp) REVERT: F 87 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8159 (mm-40) REVERT: F 95 ILE cc_start: 0.7940 (mp) cc_final: 0.7726 (mt) REVERT: F 126 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8536 (pttt) REVERT: F 141 ASP cc_start: 0.8008 (t0) cc_final: 0.7773 (t70) REVERT: F 145 ILE cc_start: 0.7535 (mt) cc_final: 0.7297 (pp) REVERT: F 232 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7947 (mtt-85) REVERT: G 46 ARG cc_start: 0.6370 (ttm170) cc_final: 0.5746 (ttt-90) REVERT: G 95 ILE cc_start: 0.7848 (mp) cc_final: 0.7636 (mt) REVERT: G 126 LYS cc_start: 0.8843 (ptpp) cc_final: 0.8603 (pttt) REVERT: G 145 ILE cc_start: 0.7596 (mt) cc_final: 0.7253 (pp) REVERT: G 270 LYS cc_start: 0.8881 (tttt) cc_final: 0.8449 (tttp) outliers start: 49 outliers final: 24 residues processed: 255 average time/residue: 1.3746 time to fit residues: 379.3749 Evaluate side-chains 230 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 132 optimal weight: 7.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 197 GLN G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13972 Z= 0.335 Angle : 0.716 10.406 19033 Z= 0.386 Chirality : 0.048 0.154 2324 Planarity : 0.006 0.071 2380 Dihedral : 6.818 59.445 1964 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.59 % Favored : 92.64 % Rotamer: Outliers : 3.02 % Allowed : 22.60 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1806 helix: 1.59 (0.17), residues: 945 sheet: -1.59 (0.29), residues: 273 loop : -0.76 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 130 HIS 0.002 0.001 HIS A 147 PHE 0.018 0.002 PHE C 63 TYR 0.014 0.002 TYR E 173 ARG 0.005 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 215 time to evaluate : 1.668 Fit side-chains REVERT: A 46 ARG cc_start: 0.6391 (ttm170) cc_final: 0.5837 (ttt90) REVERT: A 87 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8150 (mm-40) REVERT: A 145 ILE cc_start: 0.7870 (mt) cc_final: 0.7633 (OUTLIER) REVERT: B 46 ARG cc_start: 0.6193 (ttm170) cc_final: 0.5489 (ttt90) REVERT: B 145 ILE cc_start: 0.7784 (mt) cc_final: 0.7500 (pp) REVERT: C 46 ARG cc_start: 0.6627 (ttm170) cc_final: 0.5848 (ttt90) REVERT: C 87 GLN cc_start: 0.8723 (mm-40) cc_final: 0.7966 (mm-40) REVERT: C 145 ILE cc_start: 0.7958 (mt) cc_final: 0.7418 (pp) REVERT: C 194 LYS cc_start: 0.8131 (tppt) cc_final: 0.7810 (tptp) REVERT: D 46 ARG cc_start: 0.6482 (ttm170) cc_final: 0.5747 (ttt-90) REVERT: D 95 ILE cc_start: 0.7937 (mp) cc_final: 0.7609 (mt) REVERT: D 126 LYS cc_start: 0.8847 (ptpp) cc_final: 0.8633 (pttt) REVERT: D 145 ILE cc_start: 0.7835 (mt) cc_final: 0.7477 (pp) REVERT: E 46 ARG cc_start: 0.6292 (ttm170) cc_final: 0.5559 (ttp80) REVERT: E 145 ILE cc_start: 0.7910 (mt) cc_final: 0.7433 (pp) REVERT: F 46 ARG cc_start: 0.6400 (ttm170) cc_final: 0.5951 (mtp180) REVERT: F 51 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7136 (mp) REVERT: F 87 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8168 (mm-40) REVERT: F 145 ILE cc_start: 0.7734 (mt) cc_final: 0.7419 (pp) REVERT: F 270 LYS cc_start: 0.8988 (tttm) cc_final: 0.8601 (tttp) REVERT: G 46 ARG cc_start: 0.6503 (ttm170) cc_final: 0.5829 (ttt-90) REVERT: G 126 LYS cc_start: 0.8915 (ptpp) cc_final: 0.8699 (pttt) REVERT: G 145 ILE cc_start: 0.7817 (mt) cc_final: 0.7465 (pp) REVERT: G 270 LYS cc_start: 0.8890 (tttt) cc_final: 0.8419 (tttp) outliers start: 44 outliers final: 31 residues processed: 247 average time/residue: 1.4299 time to fit residues: 381.7103 Evaluate side-chains 235 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.9980 chunk 124 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 195 ASN D 197 GLN F 195 ASN F 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13972 Z= 0.167 Angle : 0.605 8.882 19033 Z= 0.323 Chirality : 0.044 0.143 2324 Planarity : 0.005 0.068 2380 Dihedral : 6.279 59.739 1964 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.20 % Favored : 93.02 % Rotamer: Outliers : 4.53 % Allowed : 22.73 % Favored : 72.73 % 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: 0.91 (0.21), residues: 1806 helix: 1.98 (0.17), residues: 945 sheet: -1.49 (0.29), residues: 273 loop : -0.55 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 241 HIS 0.002 0.001 HIS F 147 PHE 0.015 0.001 PHE C 63 TYR 0.008 0.001 TYR E 173 ARG 0.002 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 208 time to evaluate : 1.674 Fit side-chains REVERT: A 46 ARG cc_start: 0.6392 (ttm170) cc_final: 0.5841 (ttt90) REVERT: A 51 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 87 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8130 (mm-40) REVERT: A 232 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7819 (mtt-85) REVERT: B 46 ARG cc_start: 0.6188 (ttm170) cc_final: 0.5482 (ttt90) REVERT: B 145 ILE cc_start: 0.7725 (mt) cc_final: 0.7513 (pp) REVERT: B 232 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: C 46 ARG cc_start: 0.6633 (ttm170) cc_final: 0.5915 (ttt90) REVERT: C 87 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8082 (mm-40) REVERT: C 145 ILE cc_start: 0.7853 (mt) cc_final: 0.7334 (pp) REVERT: C 194 LYS cc_start: 0.7975 (tppt) cc_final: 0.7617 (tptp) REVERT: C 232 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7861 (mtt-85) REVERT: D 46 ARG cc_start: 0.6418 (ttm170) cc_final: 0.5635 (ttp80) REVERT: D 51 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7386 (mp) REVERT: D 95 ILE cc_start: 0.7899 (mp) cc_final: 0.7572 (mt) REVERT: D 123 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7186 (mtt90) REVERT: D 126 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8556 (pttt) REVERT: D 145 ILE cc_start: 0.7670 (mt) cc_final: 0.7372 (pp) REVERT: D 232 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7847 (mtt-85) REVERT: E 46 ARG cc_start: 0.6290 (ttm170) cc_final: 0.5554 (ttp80) REVERT: E 123 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7472 (mtt90) REVERT: E 145 ILE cc_start: 0.7743 (mt) cc_final: 0.7353 (pp) REVERT: E 216 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8513 (m) REVERT: F 46 ARG cc_start: 0.6373 (ttm170) cc_final: 0.5970 (mtp-110) REVERT: F 51 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7079 (mp) REVERT: F 87 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8209 (mm-40) REVERT: F 141 ASP cc_start: 0.8045 (t0) cc_final: 0.7838 (t0) REVERT: F 145 ILE cc_start: 0.7658 (mt) cc_final: 0.7427 (pp) REVERT: F 232 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7910 (mtt-85) REVERT: F 270 LYS cc_start: 0.8923 (tttm) cc_final: 0.8573 (tttp) REVERT: G 46 ARG cc_start: 0.6499 (ttm170) cc_final: 0.5822 (ttt-90) REVERT: G 145 ILE cc_start: 0.7660 (mt) cc_final: 0.7334 (pp) REVERT: G 270 LYS cc_start: 0.8864 (tttt) cc_final: 0.8427 (tttp) outliers start: 66 outliers final: 25 residues processed: 262 average time/residue: 1.3388 time to fit residues: 381.1495 Evaluate side-chains 239 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 130 optimal weight: 30.0000 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 89 optimal weight: 0.0170 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN F 195 ASN F 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13972 Z= 0.149 Angle : 0.565 7.968 19033 Z= 0.300 Chirality : 0.043 0.153 2324 Planarity : 0.005 0.065 2380 Dihedral : 5.739 59.406 1952 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.37 % Favored : 93.85 % Rotamer: Outliers : 3.71 % Allowed : 23.35 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1806 helix: 2.17 (0.17), residues: 952 sheet: -1.42 (0.28), residues: 280 loop : -0.31 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.012 0.001 PHE D 63 TYR 0.006 0.001 TYR E 173 ARG 0.006 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 202 time to evaluate : 1.767 Fit side-chains REVERT: A 46 ARG cc_start: 0.6397 (ttm170) cc_final: 0.5843 (ttt90) REVERT: A 87 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8122 (mm-40) REVERT: A 184 ASP cc_start: 0.7126 (m-30) cc_final: 0.6852 (m-30) REVERT: A 232 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8274 (mpt-90) REVERT: B 46 ARG cc_start: 0.6194 (ttm170) cc_final: 0.5486 (ttt90) REVERT: B 232 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7364 (mtt-85) REVERT: C 46 ARG cc_start: 0.6682 (ttm170) cc_final: 0.5977 (ttt90) REVERT: C 51 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7189 (mp) REVERT: C 87 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8214 (mm-40) REVERT: C 194 LYS cc_start: 0.8026 (tppt) cc_final: 0.7665 (tptp) REVERT: C 232 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7463 (mtt-85) REVERT: D 46 ARG cc_start: 0.6443 (ttm170) cc_final: 0.5638 (ttp80) REVERT: D 95 ILE cc_start: 0.7833 (mp) cc_final: 0.7504 (mt) REVERT: D 123 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7170 (mtt90) REVERT: D 126 LYS cc_start: 0.8752 (ptpp) cc_final: 0.8533 (pttt) REVERT: D 232 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7611 (mtt-85) REVERT: E 46 ARG cc_start: 0.6314 (ttm170) cc_final: 0.5549 (ttp80) REVERT: E 51 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7197 (mp) REVERT: E 145 ILE cc_start: 0.7644 (mt) cc_final: 0.7301 (pp) REVERT: F 51 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7084 (mp) REVERT: F 83 MET cc_start: 0.8254 (ttm) cc_final: 0.8005 (ttp) REVERT: F 87 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8205 (mm-40) REVERT: F 232 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7471 (mtt-85) REVERT: G 46 ARG cc_start: 0.6456 (ttm170) cc_final: 0.5774 (ttt-90) REVERT: G 51 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7299 (mp) REVERT: G 270 LYS cc_start: 0.8891 (tttt) cc_final: 0.8453 (tttp) outliers start: 54 outliers final: 30 residues processed: 245 average time/residue: 1.3116 time to fit residues: 349.5079 Evaluate side-chains 233 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN G 41 ASN G 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13972 Z= 0.220 Angle : 0.618 8.940 19033 Z= 0.331 Chirality : 0.045 0.153 2324 Planarity : 0.005 0.066 2380 Dihedral : 5.272 56.993 1944 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.76 % Favored : 92.47 % Rotamer: Outliers : 3.85 % Allowed : 23.70 % Favored : 72.46 % 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: 1.39 (0.21), residues: 1806 helix: 2.19 (0.17), residues: 952 sheet: -0.70 (0.30), residues: 280 loop : -0.33 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.015 0.002 PHE C 63 TYR 0.011 0.001 TYR E 173 ARG 0.009 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 200 time to evaluate : 1.694 Fit side-chains REVERT: A 46 ARG cc_start: 0.6404 (ttm170) cc_final: 0.5844 (ttt90) REVERT: A 87 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8184 (mm-40) REVERT: A 232 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7917 (mtt-85) REVERT: B 46 ARG cc_start: 0.6195 (ttm170) cc_final: 0.5477 (ttt90) REVERT: B 232 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7802 (mtt-85) REVERT: C 46 ARG cc_start: 0.6627 (ttm170) cc_final: 0.5840 (ttt90) REVERT: C 51 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7091 (mp) REVERT: C 87 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8160 (mm-40) REVERT: C 194 LYS cc_start: 0.8008 (tppt) cc_final: 0.7642 (tptp) REVERT: C 232 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8009 (mtt-85) REVERT: C 250 LYS cc_start: 0.7302 (mtmt) cc_final: 0.7053 (mttm) REVERT: D 46 ARG cc_start: 0.6510 (ttm170) cc_final: 0.5745 (ttt-90) REVERT: D 51 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7285 (mp) REVERT: D 95 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7563 (mt) REVERT: D 123 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7307 (mtt90) REVERT: D 126 LYS cc_start: 0.8808 (ptpp) cc_final: 0.8573 (pttt) REVERT: D 232 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7992 (mtt-85) REVERT: E 46 ARG cc_start: 0.6319 (ttm170) cc_final: 0.5561 (ttp80) REVERT: E 51 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7122 (mp) REVERT: E 145 ILE cc_start: 0.7670 (mt) cc_final: 0.7303 (pp) REVERT: F 46 ARG cc_start: 0.6658 (ttm110) cc_final: 0.6337 (mtp-110) REVERT: F 51 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7092 (mp) REVERT: F 87 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8247 (mm-40) REVERT: F 145 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7049 (pp) REVERT: F 232 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8002 (mtt-85) REVERT: G 46 ARG cc_start: 0.6463 (ttm170) cc_final: 0.5780 (ttt-90) REVERT: G 51 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7304 (mp) REVERT: G 270 LYS cc_start: 0.8840 (tttt) cc_final: 0.8403 (tttp) outliers start: 56 outliers final: 32 residues processed: 245 average time/residue: 1.3592 time to fit residues: 361.1478 Evaluate side-chains 243 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 198 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN F 197 GLN G 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13972 Z= 0.194 Angle : 0.601 8.606 19033 Z= 0.322 Chirality : 0.044 0.162 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.231 57.755 1944 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.26 % Favored : 92.97 % Rotamer: Outliers : 3.71 % Allowed : 24.04 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.21), residues: 1806 helix: 2.25 (0.17), residues: 952 sheet: -0.65 (0.30), residues: 280 loop : -0.27 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.014 0.002 PHE C 63 TYR 0.009 0.001 TYR E 173 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 199 time to evaluate : 1.419 Fit side-chains REVERT: A 46 ARG cc_start: 0.6427 (ttm170) cc_final: 0.5855 (ttt90) REVERT: A 87 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8198 (mm-40) REVERT: A 184 ASP cc_start: 0.6550 (OUTLIER) cc_final: 0.6221 (m-30) REVERT: A 195 ASN cc_start: 0.8532 (t0) cc_final: 0.8066 (t0) REVERT: A 232 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7824 (mtt-85) REVERT: B 46 ARG cc_start: 0.6197 (ttm170) cc_final: 0.5478 (ttt90) REVERT: B 232 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7699 (mtt-85) REVERT: C 46 ARG cc_start: 0.6628 (ttm170) cc_final: 0.5863 (ttt90) REVERT: C 51 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7097 (mp) REVERT: C 87 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8233 (mm-40) REVERT: C 194 LYS cc_start: 0.7995 (tppt) cc_final: 0.7628 (tptp) REVERT: C 232 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7893 (mtt-85) REVERT: D 46 ARG cc_start: 0.6558 (ttm170) cc_final: 0.5752 (ttt-90) REVERT: D 51 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7284 (mp) REVERT: D 95 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7558 (mt) REVERT: D 123 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7068 (mtt90) REVERT: D 126 LYS cc_start: 0.8792 (ptpp) cc_final: 0.8562 (pttt) REVERT: D 232 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7872 (mtt-85) REVERT: E 46 ARG cc_start: 0.6339 (ttm170) cc_final: 0.5585 (ttp80) REVERT: E 51 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7121 (mp) REVERT: F 46 ARG cc_start: 0.6698 (ttm110) cc_final: 0.6418 (mtp-110) REVERT: F 51 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7153 (mp) REVERT: F 87 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8337 (mm-40) REVERT: F 145 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7126 (pp) REVERT: F 232 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7888 (mtt-85) REVERT: G 46 ARG cc_start: 0.6464 (ttm170) cc_final: 0.5780 (ttt-90) REVERT: G 51 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7221 (mp) REVERT: G 270 LYS cc_start: 0.8835 (tttt) cc_final: 0.8400 (tttp) outliers start: 54 outliers final: 28 residues processed: 243 average time/residue: 1.3813 time to fit residues: 363.3865 Evaluate side-chains 235 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 193 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.0970 chunk 70 optimal weight: 0.4980 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 0.0060 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13972 Z= 0.171 Angle : 0.580 8.310 19033 Z= 0.310 Chirality : 0.044 0.194 2324 Planarity : 0.005 0.066 2380 Dihedral : 5.072 58.124 1943 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.15 % Favored : 93.08 % Rotamer: Outliers : 3.57 % Allowed : 24.18 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1806 helix: 2.34 (0.17), residues: 952 sheet: -0.58 (0.30), residues: 280 loop : -0.22 (0.30), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.011 0.001 PHE D 63 TYR 0.008 0.001 TYR E 173 ARG 0.007 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 1.490 Fit side-chains REVERT: A 46 ARG cc_start: 0.6428 (ttm170) cc_final: 0.5854 (ttt90) REVERT: A 87 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8196 (mm-40) REVERT: A 195 ASN cc_start: 0.8539 (t0) cc_final: 0.8081 (t0) REVERT: B 46 ARG cc_start: 0.6198 (ttm170) cc_final: 0.5480 (ttt90) REVERT: B 232 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7494 (mtt-85) REVERT: C 46 ARG cc_start: 0.6625 (ttm170) cc_final: 0.5859 (ttt90) REVERT: C 51 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7099 (mp) REVERT: C 87 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8264 (mm-40) REVERT: C 194 LYS cc_start: 0.7995 (tppt) cc_final: 0.7625 (tptp) REVERT: C 232 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7664 (mtt-85) REVERT: D 46 ARG cc_start: 0.6578 (ttm170) cc_final: 0.5753 (ttt-90) REVERT: D 51 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7311 (mp) REVERT: D 95 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7516 (mt) REVERT: D 123 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7174 (mtt90) REVERT: D 126 LYS cc_start: 0.8782 (ptpp) cc_final: 0.8555 (pttt) REVERT: D 232 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7734 (mtt-85) REVERT: E 46 ARG cc_start: 0.6361 (ttm170) cc_final: 0.5612 (ttp80) REVERT: E 51 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7175 (mp) REVERT: F 46 ARG cc_start: 0.6556 (ttm110) cc_final: 0.6317 (mtp-110) REVERT: F 51 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7129 (mp) REVERT: F 87 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8129 (mm-40) REVERT: F 145 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7123 (pp) REVERT: F 232 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7712 (mtt-85) REVERT: G 46 ARG cc_start: 0.6466 (ttm170) cc_final: 0.5781 (ttt-90) REVERT: G 51 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7152 (mp) REVERT: G 232 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7194 (mtt-85) REVERT: G 270 LYS cc_start: 0.8827 (tttt) cc_final: 0.8395 (tttp) outliers start: 52 outliers final: 30 residues processed: 240 average time/residue: 1.3730 time to fit residues: 356.9713 Evaluate side-chains 242 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 199 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.8980 chunk 168 optimal weight: 0.0470 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 0.0070 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN C 197 GLN F 197 GLN G 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13972 Z= 0.144 Angle : 0.546 7.753 19033 Z= 0.290 Chirality : 0.043 0.188 2324 Planarity : 0.004 0.064 2380 Dihedral : 4.931 58.758 1943 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.32 % Favored : 93.91 % Rotamer: Outliers : 3.37 % Allowed : 24.38 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.21), residues: 1806 helix: 2.39 (0.17), residues: 959 sheet: -0.71 (0.30), residues: 294 loop : 0.00 (0.31), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 241 HIS 0.002 0.001 HIS F 147 PHE 0.009 0.001 PHE D 63 TYR 0.005 0.001 TYR E 173 ARG 0.005 0.000 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 1.424 Fit side-chains REVERT: A 46 ARG cc_start: 0.6422 (ttm170) cc_final: 0.5848 (ttt90) REVERT: A 87 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8101 (mm-40) REVERT: A 195 ASN cc_start: 0.8531 (t0) cc_final: 0.8116 (t0) REVERT: B 46 ARG cc_start: 0.6119 (ttm170) cc_final: 0.5393 (ttt90) REVERT: C 46 ARG cc_start: 0.6689 (ttm170) cc_final: 0.5913 (ttt90) REVERT: C 51 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7096 (mp) REVERT: C 87 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8376 (mm-40) REVERT: C 194 LYS cc_start: 0.7999 (tppt) cc_final: 0.7679 (tptp) REVERT: D 46 ARG cc_start: 0.6546 (ttm170) cc_final: 0.5683 (ttp80) REVERT: D 95 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7460 (mt) REVERT: D 123 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7103 (mtt90) REVERT: D 126 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8543 (pttt) REVERT: D 232 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7149 (mtt-85) REVERT: E 46 ARG cc_start: 0.6258 (ttm170) cc_final: 0.5562 (ttp80) REVERT: E 51 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7172 (mp) REVERT: F 46 ARG cc_start: 0.6514 (ttm110) cc_final: 0.6272 (mtp-110) REVERT: F 51 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7086 (mp) REVERT: F 83 MET cc_start: 0.8277 (ttm) cc_final: 0.8023 (ttp) REVERT: F 87 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8162 (mm-40) REVERT: F 145 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7200 (tp) REVERT: F 154 ASP cc_start: 0.6991 (t70) cc_final: 0.6655 (t70) REVERT: G 46 ARG cc_start: 0.6477 (ttm170) cc_final: 0.5790 (ttt-90) REVERT: G 51 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7257 (mp) REVERT: G 239 ASP cc_start: 0.8717 (m-30) cc_final: 0.8454 (m-30) REVERT: G 270 LYS cc_start: 0.8807 (tttt) cc_final: 0.8390 (tttp) outliers start: 49 outliers final: 29 residues processed: 248 average time/residue: 1.3587 time to fit residues: 365.8515 Evaluate side-chains 240 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 82 optimal weight: 0.0000 chunk 120 optimal weight: 2.9990 chunk 181 optimal weight: 0.0980 chunk 166 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN C 197 GLN F 197 GLN F 266 GLN G 41 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13972 Z= 0.146 Angle : 0.547 7.771 19033 Z= 0.290 Chirality : 0.043 0.187 2324 Planarity : 0.004 0.064 2380 Dihedral : 4.598 27.833 1939 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.09 % Favored : 94.13 % Rotamer: Outliers : 2.68 % Allowed : 25.07 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.21), residues: 1806 helix: 2.42 (0.17), residues: 959 sheet: -0.35 (0.30), residues: 280 loop : -0.07 (0.30), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 241 HIS 0.002 0.001 HIS F 147 PHE 0.008 0.001 PHE D 63 TYR 0.006 0.001 TYR E 173 ARG 0.006 0.000 ARG F 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 212 time to evaluate : 1.667 Fit side-chains REVERT: A 46 ARG cc_start: 0.6456 (ttm170) cc_final: 0.5861 (ttt90) REVERT: A 87 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8082 (mm-40) REVERT: A 195 ASN cc_start: 0.8523 (t0) cc_final: 0.8064 (t0) REVERT: B 46 ARG cc_start: 0.6117 (ttm170) cc_final: 0.5390 (ttt90) REVERT: C 46 ARG cc_start: 0.6638 (ttm170) cc_final: 0.5851 (ttt90) REVERT: C 51 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7089 (mp) REVERT: C 194 LYS cc_start: 0.8068 (tppt) cc_final: 0.7715 (tptp) REVERT: D 46 ARG cc_start: 0.6559 (ttm170) cc_final: 0.5725 (ttp80) REVERT: D 95 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7453 (mt) REVERT: D 123 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7094 (mtt90) REVERT: D 126 LYS cc_start: 0.8771 (ptpp) cc_final: 0.8546 (pttt) REVERT: D 232 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8275 (mmt180) REVERT: E 46 ARG cc_start: 0.6258 (ttm170) cc_final: 0.5561 (ttp80) REVERT: E 51 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7169 (mp) REVERT: F 46 ARG cc_start: 0.6515 (ttm110) cc_final: 0.6272 (mtp-110) REVERT: F 51 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7105 (mp) REVERT: F 87 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8169 (mm-40) REVERT: F 145 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7195 (tp) REVERT: F 154 ASP cc_start: 0.6995 (t70) cc_final: 0.6654 (t70) REVERT: G 46 ARG cc_start: 0.6475 (ttm170) cc_final: 0.5789 (ttt-90) REVERT: G 51 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7220 (mp) REVERT: G 270 LYS cc_start: 0.8805 (tttt) cc_final: 0.8385 (tttp) outliers start: 39 outliers final: 26 residues processed: 240 average time/residue: 1.3853 time to fit residues: 365.1738 Evaluate side-chains 243 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN C 197 GLN F 197 GLN G 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.099961 restraints weight = 15492.226| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.77 r_work: 0.3051 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13972 Z= 0.167 Angle : 0.565 7.931 19033 Z= 0.300 Chirality : 0.044 0.181 2324 Planarity : 0.005 0.064 2380 Dihedral : 4.648 27.385 1939 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.59 % Favored : 93.63 % Rotamer: Outliers : 2.75 % Allowed : 25.07 % Favored : 72.18 % 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: 1.77 (0.21), residues: 1806 helix: 2.40 (0.17), residues: 959 sheet: -0.40 (0.30), residues: 280 loop : -0.07 (0.30), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.010 0.001 PHE D 63 TYR 0.008 0.001 TYR E 173 ARG 0.006 0.000 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5952.85 seconds wall clock time: 105 minutes 34.54 seconds (6334.54 seconds total)