Starting phenix.real_space_refine on Sat Feb 17 12:10:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/02_2024/7f3e_31432.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/02_2024/7f3e_31432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/02_2024/7f3e_31432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/02_2024/7f3e_31432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/02_2024/7f3e_31432.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/02_2024/7f3e_31432.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 84 5.16 5 C 11868 2.51 5 N 3168 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H ARG 133": "NH1" <-> "NH2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ARG 125": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J GLU 60": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J ARG 125": "NH1" <-> "NH2" Residue "J ARG 129": "NH1" <-> "NH2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I ARG 125": "NH1" <-> "NH2" Residue "I ARG 129": "NH1" <-> "NH2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L ARG 125": "NH1" <-> "NH2" Residue "L ARG 129": "NH1" <-> "NH2" Residue "L ARG 133": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 39": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K ARG 125": "NH1" <-> "NH2" Residue "K ARG 129": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18564 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "H" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Time building chain proxies: 9.49, per 1000 atoms: 0.51 Number of scatterers: 18564 At special positions: 0 Unit cell: (102.96, 157.52, 136.4, 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 84 16.00 O 3444 8.00 N 3168 7.00 C 11868 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: 6.57 Conformation dependent library (CDL) restraints added in 3.1 seconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 18 sheets defined 70.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL E 10 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE E 11 " --> pdb=" O THR E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 7 through 11' Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.741A pdb=" N ASN E 37 " --> pdb=" O HIS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 133 Processing helix chain 'E' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'F' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL F 10 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE F 11 " --> pdb=" O THR F 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 7 through 11' Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.741A pdb=" N ASN F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 133 Processing helix chain 'F' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 removed outlier: 4.165A pdb=" N THR F 165 " --> pdb=" O GLU F 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP F 166 " --> pdb=" O GLY F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL C 10 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 11 " --> pdb=" O THR C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.743A pdb=" N ASN C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 133 Processing helix chain 'C' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 4.165A pdb=" N THR C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL D 10 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 11 " --> pdb=" O THR D 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 7 through 11' Processing helix chain 'D' and resid 13 through 20 Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.740A pdb=" N ASN D 37 " --> pdb=" O HIS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 61 through 68 removed outlier: 3.874A pdb=" N PHE D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 114 removed outlier: 3.837A pdb=" N TYR D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 133 Processing helix chain 'D' and resid 139 through 152 removed outlier: 4.013A pdb=" N VAL D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 4.164A pdb=" N THR D 165 " --> pdb=" O GLU D 161 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'A' and resid 7 through 11 removed outlier: 3.970A pdb=" N VAL A 10 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 11 " --> pdb=" O THR A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 7 through 11' Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN A 37 " --> pdb=" O HIS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 114 removed outlier: 3.839A pdb=" N TYR A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 133 Processing helix chain 'A' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL B 10 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 11 " --> pdb=" O THR B 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 7 through 11' Processing helix chain 'B' and resid 13 through 20 Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN B 37 " --> pdb=" O HIS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.872A pdb=" N PHE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 133 Processing helix chain 'B' and resid 139 through 152 removed outlier: 4.014A pdb=" N VAL B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 4.164A pdb=" N THR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'H' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL H 10 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE H 11 " --> pdb=" O THR H 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 7 through 11' Processing helix chain 'H' and resid 13 through 20 Processing helix chain 'H' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN H 37 " --> pdb=" O HIS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 61 through 68 removed outlier: 3.874A pdb=" N PHE H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 114 removed outlier: 3.837A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 133 Processing helix chain 'H' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL H 143 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR H 165 " --> pdb=" O GLU H 161 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 190 Processing helix chain 'G' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL G 10 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE G 11 " --> pdb=" O THR G 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 7 through 11' Processing helix chain 'G' and resid 13 through 20 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN G 37 " --> pdb=" O HIS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 61 through 68 removed outlier: 3.874A pdb=" N PHE G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 133 Processing helix chain 'G' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL G 143 " --> pdb=" O SER G 139 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 removed outlier: 4.164A pdb=" N THR G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP G 166 " --> pdb=" O GLY G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 190 Processing helix chain 'J' and resid 7 through 11 removed outlier: 3.970A pdb=" N VAL J 10 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE J 11 " --> pdb=" O THR J 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 7 through 11' Processing helix chain 'J' and resid 13 through 20 Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN J 37 " --> pdb=" O HIS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 56 Processing helix chain 'J' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 133 Processing helix chain 'J' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP J 166 " --> pdb=" O GLY J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 190 Processing helix chain 'I' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL I 10 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE I 11 " --> pdb=" O THR I 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 7 through 11' Processing helix chain 'I' and resid 13 through 20 Processing helix chain 'I' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN I 37 " --> pdb=" O HIS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 56 Processing helix chain 'I' and resid 61 through 68 removed outlier: 3.872A pdb=" N PHE I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR I 95 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 133 Processing helix chain 'I' and resid 139 through 152 removed outlier: 4.013A pdb=" N VAL I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 171 removed outlier: 4.165A pdb=" N THR I 165 " --> pdb=" O GLU I 161 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP I 166 " --> pdb=" O GLY I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 190 Processing helix chain 'L' and resid 7 through 11 removed outlier: 3.970A pdb=" N VAL L 10 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE L 11 " --> pdb=" O THR L 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 7 through 11' Processing helix chain 'L' and resid 13 through 20 Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN L 37 " --> pdb=" O HIS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 56 Processing helix chain 'L' and resid 61 through 68 removed outlier: 3.875A pdb=" N PHE L 65 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 114 removed outlier: 3.840A pdb=" N TYR L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 133 Processing helix chain 'L' and resid 139 through 152 removed outlier: 4.013A pdb=" N VAL L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR L 165 " --> pdb=" O GLU L 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP L 166 " --> pdb=" O GLY L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 190 Processing helix chain 'K' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL K 10 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE K 11 " --> pdb=" O THR K 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 7 through 11' Processing helix chain 'K' and resid 13 through 20 Processing helix chain 'K' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN K 37 " --> pdb=" O HIS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 68 removed outlier: 3.874A pdb=" N PHE K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 removed outlier: 3.839A pdb=" N TYR K 95 " --> pdb=" O GLU K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 133 Processing helix chain 'K' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL K 143 " --> pdb=" O SER K 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 171 removed outlier: 4.165A pdb=" N THR K 165 " --> pdb=" O GLU K 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP K 166 " --> pdb=" O GLY K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 190 Processing sheet with id=AA1, first strand: chain 'E' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS E 70 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE E 4 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 80 through 82 Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS F 70 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE F 4 " --> pdb=" O TYR F 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS C 70 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE C 4 " --> pdb=" O TYR C 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 72 removed outlier: 3.860A pdb=" N LYS D 70 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE D 4 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS A 70 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 4 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS B 70 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B 4 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 69 through 72 removed outlier: 3.860A pdb=" N LYS H 70 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE H 4 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AB3, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.862A pdb=" N LYS G 70 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE G 4 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 69 through 72 removed outlier: 3.860A pdb=" N LYS J 70 " --> pdb=" O PHE J 42 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE J 4 " --> pdb=" O TYR J 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 80 through 82 Processing sheet with id=AB6, first strand: chain 'I' and resid 69 through 72 removed outlier: 3.860A pdb=" N LYS I 70 " --> pdb=" O PHE I 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE I 4 " --> pdb=" O TYR I 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS L 70 " --> pdb=" O PHE L 42 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE L 4 " --> pdb=" O TYR L 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 80 through 82 Processing sheet with id=AB9, first strand: chain 'K' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS K 70 " --> pdb=" O PHE K 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE K 4 " --> pdb=" O TYR K 43 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6156 1.34 - 1.46: 3204 1.46 - 1.57: 9372 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 18888 Sorted by residual: bond pdb=" CB VAL L 143 " pdb=" CG2 VAL L 143 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG1 ILE I 90 " pdb=" CD1 ILE I 90 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.03e+00 bond pdb=" CB VAL C 143 " pdb=" CG2 VAL C 143 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CG1 ILE K 90 " pdb=" CD1 ILE K 90 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.01e+00 bond pdb=" CB VAL B 143 " pdb=" CG2 VAL B 143 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 ... (remaining 18883 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.76: 300 105.76 - 112.82: 9984 112.82 - 119.89: 6506 119.89 - 126.96: 8482 126.96 - 134.03: 156 Bond angle restraints: 25428 Sorted by residual: angle pdb=" N THR K 12 " pdb=" CA THR K 12 " pdb=" C THR K 12 " ideal model delta sigma weight residual 114.56 111.72 2.84 1.27e+00 6.20e-01 4.98e+00 angle pdb=" N THR I 12 " pdb=" CA THR I 12 " pdb=" C THR I 12 " ideal model delta sigma weight residual 114.56 111.76 2.80 1.27e+00 6.20e-01 4.87e+00 angle pdb=" N THR L 12 " pdb=" CA THR L 12 " pdb=" C THR L 12 " ideal model delta sigma weight residual 114.56 111.76 2.80 1.27e+00 6.20e-01 4.85e+00 angle pdb=" N GLU I 60 " pdb=" CA GLU I 60 " pdb=" CB GLU I 60 " ideal model delta sigma weight residual 113.65 110.42 3.23 1.47e+00 4.63e-01 4.83e+00 angle pdb=" N THR E 12 " pdb=" CA THR E 12 " pdb=" C THR E 12 " ideal model delta sigma weight residual 114.56 111.77 2.79 1.27e+00 6.20e-01 4.82e+00 ... (remaining 25423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 9739 14.72 - 29.44: 1301 29.44 - 44.16: 312 44.16 - 58.88: 108 58.88 - 73.60: 48 Dihedral angle restraints: 11508 sinusoidal: 4896 harmonic: 6612 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N THR B 12 " pdb=" CA THR B 12 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE J 11 " pdb=" C PHE J 11 " pdb=" N THR J 12 " pdb=" CA THR J 12 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE E 11 " pdb=" C PHE E 11 " pdb=" N THR E 12 " pdb=" CA THR E 12 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 11505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1706 0.033 - 0.066: 747 0.066 - 0.099: 242 0.099 - 0.131: 101 0.131 - 0.164: 36 Chirality restraints: 2832 Sorted by residual: chirality pdb=" CB ILE F 16 " pdb=" CA ILE F 16 " pdb=" CG1 ILE F 16 " pdb=" CG2 ILE F 16 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CB ILE C 16 " pdb=" CA ILE C 16 " pdb=" CG1 ILE C 16 " pdb=" CG2 ILE C 16 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB ILE G 16 " pdb=" CA ILE G 16 " pdb=" CG1 ILE G 16 " pdb=" CG2 ILE G 16 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 2829 not shown) Planarity restraints: 3252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 73 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO G 74 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO G 74 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 73 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO F 74 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 74 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 73 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 74 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " 0.033 5.00e-02 4.00e+02 ... (remaining 3249 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3704 2.77 - 3.30: 18450 3.30 - 3.84: 29189 3.84 - 4.37: 34003 4.37 - 4.90: 58577 Nonbonded interactions: 143923 Sorted by model distance: nonbonded pdb=" O GLU K 105 " pdb=" OG1 THR K 108 " model vdw 2.242 2.440 nonbonded pdb=" O GLU B 105 " pdb=" OG1 THR B 108 " model vdw 2.242 2.440 nonbonded pdb=" O GLU D 105 " pdb=" OG1 THR D 108 " model vdw 2.243 2.440 nonbonded pdb=" O GLU J 105 " pdb=" OG1 THR J 108 " model vdw 2.243 2.440 nonbonded pdb=" O GLU A 105 " pdb=" OG1 THR A 108 " model vdw 2.243 2.440 ... (remaining 143918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 6.770 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 45.840 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 : 0.005 0.040 18888 Z= 0.330 Angle : 0.709 5.179 25428 Z= 0.426 Chirality : 0.045 0.164 2832 Planarity : 0.005 0.059 3252 Dihedral : 15.180 73.599 7212 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: -0.41 (0.17), residues: 2208 helix: 0.86 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -2.50 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 166 HIS 0.002 0.001 HIS J 33 PHE 0.014 0.002 PHE A 31 TYR 0.012 0.002 TYR B 128 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ASN cc_start: 0.5555 (t0) cc_final: 0.5293 (m-40) REVERT: C 51 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6167 (mm-30) REVERT: D 55 ILE cc_start: 0.7123 (mt) cc_final: 0.6551 (mt) REVERT: D 160 ASP cc_start: 0.7527 (t70) cc_final: 0.6261 (m-30) REVERT: J 13 ASN cc_start: 0.5631 (t0) cc_final: 0.5373 (m-40) REVERT: J 51 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6178 (mm-30) REVERT: J 98 ASN cc_start: 0.7757 (m-40) cc_final: 0.7534 (m-40) REVERT: I 55 ILE cc_start: 0.7212 (mt) cc_final: 0.6674 (mt) REVERT: I 160 ASP cc_start: 0.7614 (t70) cc_final: 0.6345 (m-30) REVERT: L 160 ASP cc_start: 0.5787 (t70) cc_final: 0.5510 (m-30) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.3185 time to fit residues: 212.9853 Evaluate side-chains 255 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN J 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18888 Z= 0.198 Angle : 0.584 6.377 25428 Z= 0.318 Chirality : 0.043 0.134 2832 Planarity : 0.005 0.049 3252 Dihedral : 4.511 21.249 2520 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.10 % Allowed : 10.38 % Favored : 88.52 % 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: -0.24 (0.18), residues: 2208 helix: 0.96 (0.14), residues: 1500 sheet: -1.58 (0.46), residues: 120 loop : -2.78 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 166 HIS 0.003 0.001 HIS J 190 PHE 0.017 0.001 PHE A 77 TYR 0.029 0.001 TYR K 87 ARG 0.006 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 296 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 MET cc_start: 0.4801 (mmm) cc_final: 0.4538 (mpp) REVERT: D 51 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: J 98 ASN cc_start: 0.7794 (m-40) cc_final: 0.7483 (m110) REVERT: K 1 MET cc_start: 0.1493 (tpt) cc_final: 0.1118 (tpt) outliers start: 22 outliers final: 20 residues processed: 309 average time/residue: 0.3037 time to fit residues: 142.1861 Evaluate side-chains 256 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 235 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN C 190 HIS B 179 ASN J 179 ASN J 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18888 Z= 0.186 Angle : 0.544 5.898 25428 Z= 0.294 Chirality : 0.042 0.139 2832 Planarity : 0.004 0.042 3252 Dihedral : 4.294 20.336 2520 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.45 % Allowed : 15.12 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2208 helix: 1.18 (0.14), residues: 1488 sheet: -1.61 (0.44), residues: 120 loop : -2.80 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 166 HIS 0.009 0.001 HIS F 33 PHE 0.024 0.001 PHE J 11 TYR 0.015 0.001 TYR K 87 ARG 0.007 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 250 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4618 (OUTLIER) cc_final: 0.4289 (p90) REVERT: D 51 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: D 178 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.7078 (mtmm) REVERT: A 80 THR cc_start: 0.7364 (p) cc_final: 0.6927 (t) REVERT: B 52 MET cc_start: 0.7571 (tmm) cc_final: 0.7178 (ttp) REVERT: J 98 ASN cc_start: 0.7808 (m-40) cc_final: 0.7531 (m-40) REVERT: I 28 MET cc_start: 0.6836 (tpt) cc_final: 0.6581 (tpt) REVERT: L 80 THR cc_start: 0.7236 (p) cc_final: 0.6852 (t) REVERT: K 1 MET cc_start: 0.1507 (tpt) cc_final: 0.1306 (pmm) outliers start: 49 outliers final: 36 residues processed: 283 average time/residue: 0.2874 time to fit residues: 124.8324 Evaluate side-chains 261 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 222 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 197 optimal weight: 0.0170 chunk 208 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 overall best weight: 3.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN D 179 ASN A 179 ASN J 179 ASN L 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18888 Z= 0.371 Angle : 0.662 6.906 25428 Z= 0.354 Chirality : 0.047 0.138 2832 Planarity : 0.005 0.046 3252 Dihedral : 4.884 23.938 2520 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.54 % Allowed : 17.51 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2208 helix: 0.90 (0.14), residues: 1488 sheet: -1.64 (0.54), residues: 120 loop : -2.72 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 166 HIS 0.008 0.001 HIS F 33 PHE 0.038 0.003 PHE H 31 TYR 0.017 0.002 TYR E 150 ARG 0.006 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 237 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4904 (OUTLIER) cc_final: 0.4268 (p90) REVERT: C 67 MET cc_start: 0.4952 (mtt) cc_final: 0.4563 (mpp) REVERT: D 51 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: D 178 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7003 (mppt) REVERT: A 80 THR cc_start: 0.7543 (p) cc_final: 0.7021 (t) REVERT: B 52 MET cc_start: 0.7613 (tmm) cc_final: 0.7222 (ttp) REVERT: J 98 ASN cc_start: 0.7864 (m-40) cc_final: 0.7632 (m-40) REVERT: I 28 MET cc_start: 0.6944 (tpt) cc_final: 0.6603 (tpt) REVERT: L 80 THR cc_start: 0.7527 (p) cc_final: 0.7125 (t) REVERT: L 160 ASP cc_start: 0.6110 (t70) cc_final: 0.5858 (m-30) REVERT: K 1 MET cc_start: 0.1776 (tpt) cc_final: 0.1404 (pmm) outliers start: 91 outliers final: 53 residues processed: 301 average time/residue: 0.2749 time to fit residues: 128.5563 Evaluate side-chains 277 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 221 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN A 179 ASN J 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18888 Z= 0.195 Angle : 0.536 6.662 25428 Z= 0.290 Chirality : 0.042 0.138 2832 Planarity : 0.004 0.042 3252 Dihedral : 4.359 21.698 2520 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.64 % Allowed : 20.76 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2208 helix: 1.16 (0.14), residues: 1476 sheet: -1.94 (0.39), residues: 120 loop : -2.76 (0.20), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 166 HIS 0.009 0.001 HIS F 33 PHE 0.020 0.001 PHE J 11 TYR 0.012 0.001 TYR K 87 ARG 0.005 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 246 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4781 (OUTLIER) cc_final: 0.4156 (p90) REVERT: D 51 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 80 THR cc_start: 0.7549 (p) cc_final: 0.7192 (t) REVERT: B 52 MET cc_start: 0.7486 (tmm) cc_final: 0.7116 (ttp) REVERT: J 98 ASN cc_start: 0.7878 (m-40) cc_final: 0.7616 (m-40) REVERT: I 28 MET cc_start: 0.6902 (tpt) cc_final: 0.6621 (tpt) REVERT: L 80 THR cc_start: 0.7593 (p) cc_final: 0.7314 (t) REVERT: L 160 ASP cc_start: 0.6055 (t70) cc_final: 0.5760 (m-30) REVERT: K 1 MET cc_start: 0.1556 (tpt) cc_final: 0.1217 (pmm) outliers start: 73 outliers final: 47 residues processed: 296 average time/residue: 0.2917 time to fit residues: 133.3611 Evaluate side-chains 262 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 213 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN J 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18888 Z= 0.167 Angle : 0.514 6.355 25428 Z= 0.279 Chirality : 0.041 0.132 2832 Planarity : 0.004 0.042 3252 Dihedral : 4.166 21.261 2520 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.44 % Allowed : 21.26 % Favored : 75.30 % 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: 0.00 (0.18), residues: 2208 helix: 1.18 (0.14), residues: 1488 sheet: -1.98 (0.37), residues: 120 loop : -2.60 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 62 HIS 0.009 0.001 HIS F 33 PHE 0.021 0.001 PHE D 180 TYR 0.017 0.001 TYR L 150 ARG 0.007 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 230 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4618 (OUTLIER) cc_final: 0.4227 (p90) REVERT: C 67 MET cc_start: 0.5041 (mtt) cc_final: 0.4776 (mpp) REVERT: D 51 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 56 MET cc_start: 0.5277 (ttm) cc_final: 0.5032 (ttm) REVERT: A 80 THR cc_start: 0.7554 (p) cc_final: 0.7175 (t) REVERT: I 28 MET cc_start: 0.6873 (tpt) cc_final: 0.6563 (tpt) REVERT: L 80 THR cc_start: 0.7640 (p) cc_final: 0.7366 (t) REVERT: L 160 ASP cc_start: 0.6125 (t70) cc_final: 0.5829 (m-30) REVERT: L 189 ARG cc_start: 0.4909 (ptt180) cc_final: 0.4699 (ptm-80) outliers start: 69 outliers final: 46 residues processed: 279 average time/residue: 0.2805 time to fit residues: 121.6188 Evaluate side-chains 258 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 210 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN J 179 ASN ** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18888 Z= 0.245 Angle : 0.568 7.137 25428 Z= 0.306 Chirality : 0.043 0.141 2832 Planarity : 0.004 0.044 3252 Dihedral : 4.443 21.533 2520 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.94 % Allowed : 21.26 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2208 helix: 1.12 (0.14), residues: 1488 sheet: -2.17 (0.37), residues: 120 loop : -2.54 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 62 HIS 0.009 0.001 HIS F 33 PHE 0.024 0.002 PHE I 180 TYR 0.017 0.002 TYR L 150 ARG 0.007 0.000 ARG H 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 217 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4721 (OUTLIER) cc_final: 0.4068 (p90) REVERT: C 67 MET cc_start: 0.5016 (mtt) cc_final: 0.4641 (mpp) REVERT: D 51 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: D 120 LEU cc_start: 0.7008 (mt) cc_final: 0.6765 (mt) REVERT: A 80 THR cc_start: 0.7630 (p) cc_final: 0.7229 (t) REVERT: L 80 THR cc_start: 0.7707 (p) cc_final: 0.7311 (t) REVERT: L 160 ASP cc_start: 0.6288 (t70) cc_final: 0.5894 (m-30) outliers start: 79 outliers final: 55 residues processed: 271 average time/residue: 0.2810 time to fit residues: 120.5026 Evaluate side-chains 259 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN J 179 ASN ** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18888 Z= 0.179 Angle : 0.535 9.180 25428 Z= 0.285 Chirality : 0.042 0.148 2832 Planarity : 0.003 0.043 3252 Dihedral : 4.205 23.343 2520 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.39 % Allowed : 22.55 % Favored : 74.05 % 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: 0.05 (0.18), residues: 2208 helix: 1.18 (0.14), residues: 1488 sheet: -2.13 (0.36), residues: 120 loop : -2.44 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 166 HIS 0.010 0.001 HIS F 33 PHE 0.039 0.001 PHE H 11 TYR 0.019 0.001 TYR A 150 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 226 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4633 (OUTLIER) cc_final: 0.4213 (p90) REVERT: C 67 MET cc_start: 0.5070 (mtt) cc_final: 0.4717 (mpp) REVERT: D 51 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: D 120 LEU cc_start: 0.6900 (mt) cc_final: 0.6700 (mt) REVERT: A 70 LYS cc_start: 0.6680 (mppt) cc_final: 0.6444 (mmtm) REVERT: A 80 THR cc_start: 0.7579 (p) cc_final: 0.7236 (t) REVERT: L 80 THR cc_start: 0.7864 (p) cc_final: 0.7471 (t) REVERT: L 160 ASP cc_start: 0.6175 (t70) cc_final: 0.5840 (m-30) outliers start: 68 outliers final: 51 residues processed: 275 average time/residue: 0.2768 time to fit residues: 119.5538 Evaluate side-chains 263 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 210 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN J 179 ASN ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18888 Z= 0.257 Angle : 0.594 8.189 25428 Z= 0.315 Chirality : 0.043 0.146 2832 Planarity : 0.004 0.044 3252 Dihedral : 4.461 22.354 2520 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.59 % Allowed : 22.60 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2208 helix: 1.10 (0.14), residues: 1488 sheet: -2.29 (0.36), residues: 120 loop : -2.47 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 62 HIS 0.009 0.001 HIS F 33 PHE 0.039 0.002 PHE H 11 TYR 0.015 0.002 TYR A 150 ARG 0.008 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 210 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4682 (OUTLIER) cc_final: 0.4084 (p90) REVERT: C 67 MET cc_start: 0.5015 (mtt) cc_final: 0.4717 (mpp) REVERT: D 51 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: A 80 THR cc_start: 0.7640 (p) cc_final: 0.7168 (t) REVERT: J 67 MET cc_start: 0.4490 (OUTLIER) cc_final: 0.4121 (mtt) REVERT: L 73 SER cc_start: 0.7421 (t) cc_final: 0.6942 (p) REVERT: L 80 THR cc_start: 0.7860 (p) cc_final: 0.7460 (t) outliers start: 72 outliers final: 56 residues processed: 259 average time/residue: 0.2896 time to fit residues: 117.4524 Evaluate side-chains 260 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 201 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 0.0270 chunk 142 optimal weight: 0.0070 chunk 215 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.1258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18888 Z= 0.194 Angle : 0.559 13.561 25428 Z= 0.297 Chirality : 0.042 0.154 2832 Planarity : 0.004 0.046 3252 Dihedral : 4.301 23.843 2520 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.94 % Allowed : 23.50 % Favored : 73.55 % 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: 0.03 (0.18), residues: 2208 helix: 1.16 (0.14), residues: 1488 sheet: -2.24 (0.35), residues: 120 loop : -2.41 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 62 HIS 0.010 0.001 HIS F 33 PHE 0.033 0.002 PHE D 180 TYR 0.022 0.001 TYR B 87 ARG 0.007 0.000 ARG E 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 210 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4606 (OUTLIER) cc_final: 0.4400 (p90) REVERT: C 67 MET cc_start: 0.4995 (mtt) cc_final: 0.4652 (mpp) REVERT: D 51 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: A 80 THR cc_start: 0.7573 (p) cc_final: 0.7241 (t) REVERT: J 67 MET cc_start: 0.4465 (OUTLIER) cc_final: 0.4172 (mtt) REVERT: L 1 MET cc_start: 0.5945 (tpp) cc_final: 0.5664 (tpt) REVERT: L 73 SER cc_start: 0.7294 (t) cc_final: 0.6911 (p) REVERT: L 80 THR cc_start: 0.7879 (p) cc_final: 0.7464 (t) outliers start: 59 outliers final: 51 residues processed: 252 average time/residue: 0.2739 time to fit residues: 108.2909 Evaluate side-chains 258 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 204 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.235116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.220988 restraints weight = 22135.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.202422 restraints weight = 34012.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.202097 restraints weight = 31026.001| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18888 Z= 0.209 Angle : 0.566 7.070 25428 Z= 0.303 Chirality : 0.042 0.174 2832 Planarity : 0.004 0.046 3252 Dihedral : 4.321 24.237 2520 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.49 % Allowed : 23.15 % Favored : 73.35 % 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: 0.01 (0.18), residues: 2208 helix: 1.14 (0.14), residues: 1488 sheet: -2.31 (0.35), residues: 120 loop : -2.38 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 166 HIS 0.009 0.001 HIS F 33 PHE 0.025 0.002 PHE H 11 TYR 0.011 0.001 TYR K 87 ARG 0.007 0.000 ARG A 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.03 seconds wall clock time: 63 minutes 40.02 seconds (3820.02 seconds total)