Starting phenix.real_space_refine on Mon Mar 18 20:12:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/03_2024/6r7g_4740.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/03_2024/6r7g_4740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/03_2024/6r7g_4740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/03_2024/6r7g_4740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/03_2024/6r7g_4740.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/03_2024/6r7g_4740.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 130 5.16 5 C 13595 2.51 5 N 3687 2.21 5 O 4531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 74": "OD1" <-> "OD2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G ARG 112": "NH1" <-> "NH2" Residue "G PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H ASP 74": "OD1" <-> "OD2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I ASP 74": "OD1" <-> "OD2" Residue "I ARG 112": "NH1" <-> "NH2" Residue "I PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "J PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J ASP 74": "OD1" <-> "OD2" Residue "J ARG 112": "NH1" <-> "NH2" Residue "J PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K ASP 74": "OD1" <-> "OD2" Residue "K ARG 112": "NH1" <-> "NH2" Residue "K PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L ASP 74": "OD1" <-> "OD2" Residue "L ARG 112": "NH1" <-> "NH2" Residue "L PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "M PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M ASP 74": "OD1" <-> "OD2" Residue "M ARG 112": "NH1" <-> "NH2" Residue "M PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 204": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22012 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "B" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "C" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "E" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "G" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "H" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "I" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "J" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "K" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "L" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "M" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1580 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 14, 'TRANS': 194} Chain: "R" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1380 Classifications: {'RNA': 69} Modifications used: {'rna2p_pyr': 13, 'rna3p_pyr': 56} Link IDs: {'rna2p': 13, 'rna3p': 55} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Time building chain proxies: 11.92, per 1000 atoms: 0.54 Number of scatterers: 22012 At special positions: 0 Unit cell: (139.763, 141.417, 109.991, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 P 69 15.00 O 4531 8.00 N 3687 7.00 C 13595 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: 9.17 Conformation dependent library (CDL) restraints added in 3.9 seconds 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5174 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 0 sheets defined 59.8% alpha, 0.0% beta 0 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR A 34 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.762A pdb=" N TYR A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR A 169 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR B 34 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.762A pdb=" N TYR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE B 159 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR B 169 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 206 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL B 231 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.661A pdb=" N THR C 34 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 55 through 69 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS C 158 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE C 159 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 4.054A pdb=" N THR C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 206 Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL C 231 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR D 34 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 55 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR D 130 " --> pdb=" O PHE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS D 158 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE D 159 " --> pdb=" O GLU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR D 169 " --> pdb=" O ASN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 206 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.659A pdb=" N THR E 34 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP E 89 " --> pdb=" O ARG E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS E 158 " --> pdb=" O PRO E 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE E 159 " --> pdb=" O GLU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR E 169 " --> pdb=" O ASN E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 206 Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR F 34 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 44 Processing helix chain 'F' and resid 55 through 69 Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP F 89 " --> pdb=" O ARG F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR F 130 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS F 158 " --> pdb=" O PRO F 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE F 159 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR F 169 " --> pdb=" O ASN F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 206 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.621A pdb=" N VAL F 231 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 34 removed outlier: 3.661A pdb=" N THR G 34 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 44 Processing helix chain 'G' and resid 55 through 69 Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP G 89 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'G' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS G 158 " --> pdb=" O PRO G 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE G 159 " --> pdb=" O GLU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR G 169 " --> pdb=" O ASN G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 Processing helix chain 'G' and resid 214 through 219 Processing helix chain 'G' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL G 231 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR H 34 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 44 Processing helix chain 'H' and resid 55 through 69 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP H 89 " --> pdb=" O ARG H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'H' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR H 130 " --> pdb=" O PHE H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 Processing helix chain 'H' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS H 158 " --> pdb=" O PRO H 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE H 159 " --> pdb=" O GLU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR H 169 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 206 Processing helix chain 'H' and resid 214 through 219 Processing helix chain 'H' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL H 231 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR I 34 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 55 through 69 Processing helix chain 'I' and resid 72 through 74 No H-bonds generated for 'chain 'I' and resid 72 through 74' Processing helix chain 'I' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'I' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR I 130 " --> pdb=" O PHE I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 154 through 161 removed outlier: 3.533A pdb=" N LYS I 158 " --> pdb=" O PRO I 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE I 159 " --> pdb=" O GLU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR I 169 " --> pdb=" O ASN I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 206 Processing helix chain 'I' and resid 214 through 219 Processing helix chain 'I' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL I 231 " --> pdb=" O ALA I 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR J 34 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 44 Processing helix chain 'J' and resid 55 through 69 Processing helix chain 'J' and resid 72 through 74 No H-bonds generated for 'chain 'J' and resid 72 through 74' Processing helix chain 'J' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP J 89 " --> pdb=" O ARG J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR J 130 " --> pdb=" O PHE J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS J 158 " --> pdb=" O PRO J 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE J 159 " --> pdb=" O GLU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR J 169 " --> pdb=" O ASN J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 206 Processing helix chain 'J' and resid 214 through 219 Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL J 231 " --> pdb=" O ALA J 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR K 34 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 44 Processing helix chain 'K' and resid 55 through 69 Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 75 through 90 removed outlier: 3.618A pdb=" N ASP K 89 " --> pdb=" O ARG K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR K 130 " --> pdb=" O PHE K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 Processing helix chain 'K' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS K 158 " --> pdb=" O PRO K 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE K 159 " --> pdb=" O GLU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 169 removed outlier: 4.052A pdb=" N THR K 169 " --> pdb=" O ASN K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 206 Processing helix chain 'K' and resid 214 through 219 Processing helix chain 'K' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL K 231 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR L 34 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 44 Processing helix chain 'L' and resid 55 through 69 Processing helix chain 'L' and resid 72 through 74 No H-bonds generated for 'chain 'L' and resid 72 through 74' Processing helix chain 'L' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP L 89 " --> pdb=" O ARG L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 118 Processing helix chain 'L' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR L 130 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 Processing helix chain 'L' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS L 158 " --> pdb=" O PRO L 155 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR L 169 " --> pdb=" O ASN L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 206 Processing helix chain 'L' and resid 214 through 219 Processing helix chain 'L' and resid 227 through 231 removed outlier: 3.622A pdb=" N VAL L 231 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 34 removed outlier: 3.660A pdb=" N THR M 34 " --> pdb=" O GLY M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 44 Processing helix chain 'M' and resid 55 through 69 Processing helix chain 'M' and resid 72 through 74 No H-bonds generated for 'chain 'M' and resid 72 through 74' Processing helix chain 'M' and resid 75 through 90 removed outlier: 3.619A pdb=" N ASP M 89 " --> pdb=" O ARG M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 118 Processing helix chain 'M' and resid 122 through 130 removed outlier: 3.763A pdb=" N TYR M 130 " --> pdb=" O PHE M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 161 removed outlier: 3.532A pdb=" N LYS M 158 " --> pdb=" O PRO M 155 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE M 159 " --> pdb=" O GLU M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 169 removed outlier: 4.053A pdb=" N THR M 169 " --> pdb=" O ASN M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 206 Processing helix chain 'M' and resid 214 through 219 Processing helix chain 'M' and resid 227 through 231 removed outlier: 3.623A pdb=" N VAL M 231 " --> pdb=" O ALA M 228 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 9.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5279 1.33 - 1.45: 4789 1.45 - 1.57: 12112 1.57 - 1.69: 150 1.69 - 1.81: 221 Bond restraints: 22551 Sorted by residual: bond pdb=" CA PHE F 164 " pdb=" CB PHE F 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 5.07e+00 bond pdb=" CA PHE K 164 " pdb=" CB PHE K 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 5.05e+00 bond pdb=" CA PHE M 164 " pdb=" CB PHE M 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 4.97e+00 bond pdb=" CA PHE C 164 " pdb=" CB PHE C 164 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.51e-02 4.39e+03 4.94e+00 bond pdb=" CA PHE I 164 " pdb=" CB PHE I 164 " ideal model delta sigma weight residual 1.532 1.565 -0.033 1.51e-02 4.39e+03 4.91e+00 ... (remaining 22546 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.88: 1203 106.88 - 113.70: 12406 113.70 - 120.52: 9065 120.52 - 127.34: 8021 127.34 - 134.16: 338 Bond angle restraints: 31033 Sorted by residual: angle pdb=" CA PHE B 164 " pdb=" CB PHE B 164 " pdb=" CG PHE B 164 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.10e+01 angle pdb=" CA PHE J 164 " pdb=" CB PHE J 164 " pdb=" CG PHE J 164 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.09e+01 angle pdb=" CA PHE H 164 " pdb=" CB PHE H 164 " pdb=" CG PHE H 164 " ideal model delta sigma weight residual 113.80 117.09 -3.29 1.00e+00 1.00e+00 1.08e+01 angle pdb=" CA PHE I 164 " pdb=" CB PHE I 164 " pdb=" CG PHE I 164 " ideal model delta sigma weight residual 113.80 117.09 -3.29 1.00e+00 1.00e+00 1.08e+01 angle pdb=" CA PHE C 164 " pdb=" CB PHE C 164 " pdb=" CG PHE C 164 " ideal model delta sigma weight residual 113.80 117.08 -3.28 1.00e+00 1.00e+00 1.07e+01 ... (remaining 31028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 13406 35.52 - 71.04: 356 71.04 - 106.56: 0 106.56 - 142.08: 0 142.08 - 177.61: 1 Dihedral angle restraints: 13763 sinusoidal: 5859 harmonic: 7904 Sorted by residual: dihedral pdb=" O4' U R 29 " pdb=" C1' U R 29 " pdb=" N1 U R 29 " pdb=" C2 U R 29 " ideal model delta sinusoidal sigma weight residual -128.00 49.61 -177.61 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASP C 209 " pdb=" C ASP C 209 " pdb=" N PHE C 210 " pdb=" CA PHE C 210 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ASP H 209 " pdb=" C ASP H 209 " pdb=" N PHE H 210 " pdb=" CA PHE H 210 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 13760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2094 0.038 - 0.077: 950 0.077 - 0.115: 394 0.115 - 0.154: 117 0.154 - 0.192: 40 Chirality restraints: 3595 Sorted by residual: chirality pdb=" CA PHE D 164 " pdb=" N PHE D 164 " pdb=" C PHE D 164 " pdb=" CB PHE D 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA PHE E 164 " pdb=" N PHE E 164 " pdb=" C PHE E 164 " pdb=" CB PHE E 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 3592 not shown) Planarity restraints: 3826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 162 " 0.013 2.00e-02 2.50e+03 2.04e-02 7.26e+00 pdb=" CG PHE B 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 162 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE B 162 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 162 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 162 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 162 " 0.013 2.00e-02 2.50e+03 2.03e-02 7.24e+00 pdb=" CG PHE L 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE L 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE L 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE L 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE L 162 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.013 2.00e-02 2.50e+03 2.03e-02 7.24e+00 pdb=" CG PHE A 162 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.000 2.00e-02 2.50e+03 ... (remaining 3823 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 30 2.48 - 3.09: 14744 3.09 - 3.69: 35603 3.69 - 4.30: 54259 4.30 - 4.90: 81154 Nonbonded interactions: 185790 Sorted by model distance: nonbonded pdb=" O2 U R 65 " pdb=" O HOH R 101 " model vdw 1.880 2.440 nonbonded pdb=" OP2 U R 24 " pdb=" O HOH R 102 " model vdw 1.942 2.440 nonbonded pdb=" O2 U R 55 " pdb=" O HOH R 103 " model vdw 2.054 2.440 nonbonded pdb=" O2 U R 5 " pdb=" O HOH R 104 " model vdw 2.065 2.440 nonbonded pdb=" OP1 U R 23 " pdb=" O HOH R 105 " model vdw 2.094 2.440 ... (remaining 185785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.020 Extract box with map and model: 11.050 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 61.970 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22551 Z= 0.414 Angle : 0.850 6.978 31033 Z= 0.490 Chirality : 0.054 0.192 3595 Planarity : 0.006 0.037 3826 Dihedral : 14.935 177.605 8589 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.05 % Allowed : 3.05 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.13), residues: 2691 helix: -2.64 (0.09), residues: 1430 sheet: None (None), residues: 0 loop : -0.10 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 135 HIS 0.003 0.001 HIS B 86 PHE 0.046 0.005 PHE L 162 TYR 0.013 0.003 TYR E 130 ARG 0.006 0.001 ARG G 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 492 time to evaluate : 2.200 Fit side-chains REVERT: A 58 ASP cc_start: 0.7589 (m-30) cc_final: 0.7267 (m-30) REVERT: A 89 ASP cc_start: 0.8312 (m-30) cc_final: 0.8100 (m-30) REVERT: A 128 MET cc_start: 0.9149 (mmm) cc_final: 0.8802 (mmm) REVERT: A 177 LYS cc_start: 0.7827 (tttm) cc_final: 0.7364 (mppt) REVERT: B 69 MET cc_start: 0.7546 (ptm) cc_final: 0.7224 (ptm) REVERT: B 138 MET cc_start: 0.8514 (mtm) cc_final: 0.8288 (mtm) REVERT: C 104 TYR cc_start: 0.8253 (m-80) cc_final: 0.7973 (m-80) REVERT: D 156 GLU cc_start: 0.8239 (pm20) cc_final: 0.8018 (pm20) REVERT: F 63 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7268 (mt-10) REVERT: F 78 GLN cc_start: 0.8572 (mp10) cc_final: 0.8307 (mp10) REVERT: G 156 GLU cc_start: 0.8278 (pm20) cc_final: 0.8070 (pm20) REVERT: I 128 MET cc_start: 0.9205 (mmm) cc_final: 0.8861 (mmm) REVERT: J 175 MET cc_start: 0.8232 (tpp) cc_final: 0.8023 (tpp) REVERT: K 69 MET cc_start: 0.8038 (ptm) cc_final: 0.7826 (ptm) REVERT: L 76 MET cc_start: 0.7855 (tpp) cc_final: 0.7442 (tpp) REVERT: L 104 TYR cc_start: 0.8221 (m-80) cc_final: 0.7829 (m-80) REVERT: M 33 PHE cc_start: 0.8525 (m-80) cc_final: 0.8232 (m-80) REVERT: M 128 MET cc_start: 0.9096 (mmm) cc_final: 0.8718 (mmm) REVERT: M 141 ASN cc_start: 0.8501 (m-40) cc_final: 0.8301 (m110) outliers start: 65 outliers final: 6 residues processed: 536 average time/residue: 1.6835 time to fit residues: 997.7467 Evaluate side-chains 410 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 404 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain L residue 42 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 166 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN D 149 GLN D 166 ASN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN F 95 GLN ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 ASN G 206 GLN ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 ASN J 95 GLN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 ASN K 95 GLN ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 ASN K 206 GLN L 95 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN M 95 GLN M 166 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22551 Z= 0.261 Angle : 0.628 5.186 31033 Z= 0.349 Chirality : 0.046 0.162 3595 Planarity : 0.005 0.035 3826 Dihedral : 12.482 177.870 3955 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.27 % Allowed : 7.50 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 2691 helix: 0.05 (0.13), residues: 1443 sheet: None (None), residues: 0 loop : 0.55 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 135 HIS 0.003 0.001 HIS I 86 PHE 0.030 0.003 PHE H 164 TYR 0.017 0.002 TYR F 130 ARG 0.006 0.001 ARG K 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 424 time to evaluate : 2.352 Fit side-chains REVERT: A 58 ASP cc_start: 0.7523 (m-30) cc_final: 0.7219 (m-30) REVERT: A 89 ASP cc_start: 0.8427 (m-30) cc_final: 0.8113 (m-30) REVERT: A 128 MET cc_start: 0.9239 (mmm) cc_final: 0.8882 (mmm) REVERT: A 177 LYS cc_start: 0.7970 (tttm) cc_final: 0.7470 (mppt) REVERT: C 89 ASP cc_start: 0.8485 (m-30) cc_final: 0.8255 (m-30) REVERT: D 199 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8342 (mttm) REVERT: E 35 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8110 (mp) REVERT: H 76 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7591 (ttm) REVERT: I 128 MET cc_start: 0.9289 (mmm) cc_final: 0.8931 (mmm) REVERT: J 45 ARG cc_start: 0.7508 (mmt-90) cc_final: 0.7280 (tpt170) REVERT: J 175 MET cc_start: 0.8291 (tpp) cc_final: 0.8049 (tpp) REVERT: L 104 TYR cc_start: 0.8305 (m-80) cc_final: 0.7893 (m-80) REVERT: M 33 PHE cc_start: 0.8543 (m-80) cc_final: 0.8282 (m-80) REVERT: M 119 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7245 (mm-30) outliers start: 27 outliers final: 10 residues processed: 435 average time/residue: 1.9416 time to fit residues: 922.2201 Evaluate side-chains 424 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 411 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 241 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 194 optimal weight: 0.1980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22551 Z= 0.212 Angle : 0.557 5.062 31033 Z= 0.308 Chirality : 0.044 0.155 3595 Planarity : 0.004 0.030 3826 Dihedral : 12.208 176.549 3948 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.80 % Allowed : 8.86 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2691 helix: 0.82 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.71 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 135 HIS 0.002 0.001 HIS B 86 PHE 0.031 0.003 PHE H 164 TYR 0.015 0.002 TYR F 130 ARG 0.005 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 428 time to evaluate : 2.504 Fit side-chains REVERT: A 58 ASP cc_start: 0.7418 (m-30) cc_final: 0.7145 (m-30) REVERT: A 89 ASP cc_start: 0.8377 (m-30) cc_final: 0.8025 (m-30) REVERT: A 128 MET cc_start: 0.9240 (mmm) cc_final: 0.8934 (mmm) REVERT: A 177 LYS cc_start: 0.7956 (tttm) cc_final: 0.7506 (mppt) REVERT: B 58 ASP cc_start: 0.7638 (m-30) cc_final: 0.7313 (m-30) REVERT: B 199 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8557 (mttp) REVERT: C 58 ASP cc_start: 0.7670 (m-30) cc_final: 0.7340 (m-30) REVERT: C 89 ASP cc_start: 0.8426 (m-30) cc_final: 0.8173 (m-30) REVERT: D 199 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8278 (mttm) REVERT: E 35 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8092 (mp) REVERT: E 58 ASP cc_start: 0.7765 (m-30) cc_final: 0.7461 (m-30) REVERT: G 199 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8424 (mtpm) REVERT: H 76 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7503 (ttm) REVERT: I 128 MET cc_start: 0.9279 (mmm) cc_final: 0.8978 (mmm) REVERT: J 35 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8102 (mp) REVERT: J 45 ARG cc_start: 0.7490 (mmt-90) cc_final: 0.7279 (tpt170) REVERT: J 142 ASN cc_start: 0.8370 (t0) cc_final: 0.8138 (t0) REVERT: J 175 MET cc_start: 0.8320 (tpp) cc_final: 0.8003 (tpp) REVERT: K 177 LYS cc_start: 0.7905 (tttm) cc_final: 0.7671 (tttp) REVERT: L 65 ILE cc_start: 0.8879 (mt) cc_final: 0.8644 (mt) REVERT: M 119 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7202 (mm-30) outliers start: 17 outliers final: 7 residues processed: 435 average time/residue: 1.9412 time to fit residues: 921.2971 Evaluate side-chains 432 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 419 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 162 optimal weight: 0.0970 chunk 242 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22551 Z= 0.136 Angle : 0.460 4.956 31033 Z= 0.254 Chirality : 0.040 0.135 3595 Planarity : 0.004 0.031 3826 Dihedral : 11.872 176.178 3948 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.80 % Allowed : 9.24 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 2691 helix: 1.36 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.65 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 135 HIS 0.001 0.000 HIS K 86 PHE 0.024 0.002 PHE H 164 TYR 0.009 0.001 TYR F 130 ARG 0.006 0.000 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 450 time to evaluate : 2.414 Fit side-chains REVERT: A 89 ASP cc_start: 0.8208 (m-30) cc_final: 0.7863 (m-30) REVERT: A 177 LYS cc_start: 0.7897 (tttm) cc_final: 0.7446 (mppt) REVERT: B 69 MET cc_start: 0.7226 (ptm) cc_final: 0.6836 (mtp) REVERT: B 199 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8491 (mttp) REVERT: C 89 ASP cc_start: 0.8423 (m-30) cc_final: 0.8194 (m-30) REVERT: D 58 ASP cc_start: 0.7725 (m-30) cc_final: 0.7421 (m-30) REVERT: F 78 GLN cc_start: 0.8486 (mp10) cc_final: 0.8238 (mp10) REVERT: G 199 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8413 (mtpm) REVERT: H 76 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7513 (ttm) REVERT: J 35 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7980 (mp) REVERT: J 142 ASN cc_start: 0.8394 (t0) cc_final: 0.8116 (t0) REVERT: K 177 LYS cc_start: 0.7777 (tttm) cc_final: 0.7526 (tttp) outliers start: 17 outliers final: 4 residues processed: 453 average time/residue: 1.9513 time to fit residues: 965.8592 Evaluate side-chains 427 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 419 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 64 optimal weight: 0.0060 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22551 Z= 0.288 Angle : 0.627 5.155 31033 Z= 0.347 Chirality : 0.047 0.167 3595 Planarity : 0.005 0.034 3826 Dihedral : 12.320 176.925 3948 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.13 % Allowed : 9.33 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.16), residues: 2691 helix: 1.15 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.89 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 135 HIS 0.003 0.001 HIS B 86 PHE 0.031 0.003 PHE H 164 TYR 0.017 0.002 TYR F 130 ARG 0.005 0.001 ARG M 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 424 time to evaluate : 2.440 Fit side-chains REVERT: A 58 ASP cc_start: 0.7421 (m-30) cc_final: 0.7117 (m-30) REVERT: A 89 ASP cc_start: 0.8407 (m-30) cc_final: 0.8069 (m-30) REVERT: A 177 LYS cc_start: 0.8020 (tttm) cc_final: 0.7589 (mppt) REVERT: B 199 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8579 (mttp) REVERT: C 89 ASP cc_start: 0.8487 (m-30) cc_final: 0.8232 (m-30) REVERT: C 175 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7995 (tpp) REVERT: D 199 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8434 (mttm) REVERT: E 58 ASP cc_start: 0.7852 (m-30) cc_final: 0.7509 (m-30) REVERT: G 199 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8462 (mtpm) REVERT: H 76 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7681 (ttm) REVERT: I 128 MET cc_start: 0.9332 (mmm) cc_final: 0.8977 (mmm) REVERT: J 142 ASN cc_start: 0.8538 (t0) cc_final: 0.8177 (t0) REVERT: J 175 MET cc_start: 0.8228 (tpp) cc_final: 0.8006 (tpp) REVERT: K 177 LYS cc_start: 0.7893 (tttm) cc_final: 0.7682 (tttp) outliers start: 24 outliers final: 12 residues processed: 440 average time/residue: 1.9760 time to fit residues: 948.3914 Evaluate side-chains 431 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 414 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 143 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22551 Z= 0.323 Angle : 0.675 5.368 31033 Z= 0.374 Chirality : 0.049 0.173 3595 Planarity : 0.005 0.042 3826 Dihedral : 12.477 176.881 3948 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.17 % Allowed : 9.19 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.16), residues: 2691 helix: 1.01 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.94 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 135 HIS 0.003 0.001 HIS I 86 PHE 0.034 0.004 PHE H 164 TYR 0.018 0.003 TYR F 130 ARG 0.007 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 429 time to evaluate : 2.413 Fit side-chains REVERT: A 58 ASP cc_start: 0.7462 (m-30) cc_final: 0.7085 (m-30) REVERT: A 89 ASP cc_start: 0.8418 (m-30) cc_final: 0.8087 (m-30) REVERT: A 177 LYS cc_start: 0.8059 (tttm) cc_final: 0.7623 (mppt) REVERT: B 199 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8516 (mtpp) REVERT: C 58 ASP cc_start: 0.7714 (m-30) cc_final: 0.7406 (m-30) REVERT: C 89 ASP cc_start: 0.8518 (m-30) cc_final: 0.8260 (m-30) REVERT: C 175 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7910 (tpp) REVERT: C 199 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8486 (mttm) REVERT: D 199 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8453 (mttm) REVERT: E 35 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8140 (mp) REVERT: G 199 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8473 (mtpm) REVERT: H 76 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7554 (ttm) REVERT: I 128 MET cc_start: 0.9331 (mmm) cc_final: 0.8914 (mmm) REVERT: J 98 MET cc_start: 0.8603 (mmp) cc_final: 0.8354 (mmp) REVERT: K 177 LYS cc_start: 0.7943 (tttm) cc_final: 0.7733 (tttp) outliers start: 25 outliers final: 12 residues processed: 445 average time/residue: 1.9797 time to fit residues: 960.0780 Evaluate side-chains 434 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 415 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 143 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN I 95 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22551 Z= 0.355 Angle : 0.712 5.545 31033 Z= 0.394 Chirality : 0.051 0.182 3595 Planarity : 0.005 0.044 3826 Dihedral : 12.542 176.951 3948 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.13 % Allowed : 9.80 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2691 helix: 0.92 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.97 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 135 HIS 0.004 0.001 HIS K 86 PHE 0.036 0.004 PHE H 164 TYR 0.019 0.003 TYR F 130 ARG 0.006 0.001 ARG M 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 421 time to evaluate : 2.304 Fit side-chains REVERT: A 58 ASP cc_start: 0.7474 (m-30) cc_final: 0.7147 (m-30) REVERT: A 89 ASP cc_start: 0.8438 (m-30) cc_final: 0.8067 (m-30) REVERT: A 177 LYS cc_start: 0.8074 (tttm) cc_final: 0.7635 (mppt) REVERT: B 199 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8527 (mtpp) REVERT: C 89 ASP cc_start: 0.8524 (m-30) cc_final: 0.8305 (m-30) REVERT: C 175 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7916 (tpp) REVERT: D 199 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8335 (mttm) REVERT: E 35 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8133 (mp) REVERT: E 69 MET cc_start: 0.7675 (ptm) cc_final: 0.7316 (mtp) REVERT: G 199 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8496 (mtpm) REVERT: H 76 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7559 (ttm) REVERT: H 128 MET cc_start: 0.9177 (mmm) cc_final: 0.8851 (mmm) REVERT: I 128 MET cc_start: 0.9326 (mmm) cc_final: 0.9031 (mmm) REVERT: J 98 MET cc_start: 0.8615 (mmp) cc_final: 0.8310 (mmp) REVERT: K 177 LYS cc_start: 0.7955 (tttm) cc_final: 0.7748 (tttp) outliers start: 24 outliers final: 15 residues processed: 437 average time/residue: 2.0425 time to fit residues: 976.7253 Evaluate side-chains 433 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 412 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 143 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 225 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 chunk 126 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 201 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22551 Z= 0.145 Angle : 0.485 5.775 31033 Z= 0.268 Chirality : 0.041 0.149 3595 Planarity : 0.004 0.032 3826 Dihedral : 11.999 175.648 3948 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.66 % Allowed : 10.18 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2691 helix: 1.40 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.94 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 135 HIS 0.001 0.000 HIS K 86 PHE 0.031 0.002 PHE A 164 TYR 0.010 0.001 TYR A 130 ARG 0.006 0.000 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 432 time to evaluate : 2.466 Fit side-chains REVERT: A 89 ASP cc_start: 0.8221 (m-30) cc_final: 0.7864 (m-30) REVERT: A 177 LYS cc_start: 0.7944 (tttm) cc_final: 0.7513 (mppt) REVERT: C 89 ASP cc_start: 0.8408 (m-30) cc_final: 0.8168 (m-30) REVERT: C 199 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8367 (mttm) REVERT: E 58 ASP cc_start: 0.7778 (m-30) cc_final: 0.7381 (m-30) REVERT: E 69 MET cc_start: 0.7678 (ptm) cc_final: 0.7405 (mtp) REVERT: G 199 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8361 (mtpm) REVERT: H 69 MET cc_start: 0.7969 (ptp) cc_final: 0.7756 (ptm) REVERT: H 76 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7575 (ttm) REVERT: H 199 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8282 (mttp) REVERT: I 128 MET cc_start: 0.9274 (mmm) cc_final: 0.8981 (mmm) REVERT: K 177 LYS cc_start: 0.7893 (tttm) cc_final: 0.7669 (tttp) REVERT: M 67 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7362 (ttmm) REVERT: M 128 MET cc_start: 0.9266 (mmm) cc_final: 0.8947 (mmm) outliers start: 14 outliers final: 4 residues processed: 437 average time/residue: 2.0046 time to fit residues: 953.9171 Evaluate side-chains 437 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 429 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 225 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 143 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 156 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22551 Z= 0.245 Angle : 0.589 5.269 31033 Z= 0.326 Chirality : 0.045 0.163 3595 Planarity : 0.004 0.030 3826 Dihedral : 12.203 176.649 3948 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.80 % Allowed : 10.23 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.16), residues: 2691 helix: 1.31 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 1.00 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 135 HIS 0.002 0.001 HIS B 86 PHE 0.031 0.003 PHE K 164 TYR 0.015 0.002 TYR F 130 ARG 0.006 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 428 time to evaluate : 2.417 Fit side-chains REVERT: A 89 ASP cc_start: 0.8359 (m-30) cc_final: 0.8014 (m-30) REVERT: A 177 LYS cc_start: 0.8017 (tttm) cc_final: 0.7598 (mppt) REVERT: C 89 ASP cc_start: 0.8470 (m-30) cc_final: 0.8236 (m-30) REVERT: C 199 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8473 (mttm) REVERT: E 58 ASP cc_start: 0.7747 (m-30) cc_final: 0.7477 (m-30) REVERT: E 69 MET cc_start: 0.7676 (ptm) cc_final: 0.7311 (mtp) REVERT: G 199 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8461 (mtpm) REVERT: H 76 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7551 (ttm) REVERT: H 199 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8312 (mttp) REVERT: I 128 MET cc_start: 0.9313 (mmm) cc_final: 0.8990 (mmm) REVERT: K 177 LYS cc_start: 0.7927 (tttm) cc_final: 0.7709 (tttp) REVERT: M 67 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7485 (ttmm) outliers start: 17 outliers final: 9 residues processed: 437 average time/residue: 1.9762 time to fit residues: 942.0326 Evaluate side-chains 441 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 427 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain M residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22551 Z= 0.179 Angle : 0.520 5.957 31033 Z= 0.288 Chirality : 0.042 0.150 3595 Planarity : 0.004 0.029 3826 Dihedral : 12.051 176.192 3948 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.66 % Allowed : 10.27 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.16), residues: 2691 helix: 1.41 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.97 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 135 HIS 0.002 0.000 HIS B 86 PHE 0.031 0.002 PHE A 164 TYR 0.012 0.002 TYR F 130 ARG 0.006 0.000 ARG K 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 427 time to evaluate : 2.480 Fit side-chains REVERT: A 89 ASP cc_start: 0.8287 (m-30) cc_final: 0.7942 (m-30) REVERT: A 177 LYS cc_start: 0.7996 (tttm) cc_final: 0.7583 (mppt) REVERT: B 199 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8538 (mttp) REVERT: C 89 ASP cc_start: 0.8437 (m-30) cc_final: 0.8208 (m-30) REVERT: C 199 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8422 (mttm) REVERT: E 58 ASP cc_start: 0.7801 (m-30) cc_final: 0.7436 (m-30) REVERT: E 69 MET cc_start: 0.7681 (ptm) cc_final: 0.7350 (mtp) REVERT: F 78 GLN cc_start: 0.8458 (mp10) cc_final: 0.8227 (mp10) REVERT: G 199 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8402 (mtpm) REVERT: H 76 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7603 (ttm) REVERT: H 199 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8299 (mttp) REVERT: I 128 MET cc_start: 0.9297 (mmm) cc_final: 0.9020 (mmm) REVERT: K 177 LYS cc_start: 0.7890 (tttm) cc_final: 0.7669 (tttp) REVERT: M 57 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: M 67 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7472 (ttmm) outliers start: 14 outliers final: 7 residues processed: 434 average time/residue: 1.9736 time to fit residues: 934.0174 Evaluate side-chains 437 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 424 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain M residue 225 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** I 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114116 restraints weight = 18738.350| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 0.83 r_work: 0.3071 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22551 Z= 0.296 Angle : 0.645 5.371 31033 Z= 0.358 Chirality : 0.047 0.168 3595 Planarity : 0.005 0.034 3826 Dihedral : 12.344 176.941 3948 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.70 % Allowed : 10.13 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.16), residues: 2691 helix: 1.22 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 1.01 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 135 HIS 0.003 0.001 HIS I 86 PHE 0.031 0.003 PHE H 164 TYR 0.017 0.003 TYR F 130 ARG 0.005 0.001 ARG K 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12533.22 seconds wall clock time: 219 minutes 28.91 seconds (13168.91 seconds total)