Starting phenix.real_space_refine (version: dev) on Fri Feb 24 06:43:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/02_2023/6r7g_4740.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/02_2023/6r7g_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_4740/02_2023/6r7g_4740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/02_2023/6r7g_4740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/02_2023/6r7g_4740.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7g_4740/02_2023/6r7g_4740.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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-4877/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: 12.46, per 1000 atoms: 0.57 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: 9.12 Conformation dependent library (CDL) restraints added in 3.1 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: 5.85 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: 5.93 Time building geometry restraints manager: 9.79 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: 13250 35.52 - 71.04: 236 71.04 - 106.56: 0 106.56 - 142.08: 0 142.08 - 177.61: 1 Dihedral angle restraints: 13487 sinusoidal: 5583 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 13484 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 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. 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: 2.310 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: 12.110 Check model and map are aligned: 0.380 Process input model: 60.090 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 : 13.629 177.605 8313 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 % 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 *********************** 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 : 2.555 Fit side-chains outliers start: 65 outliers final: 6 residues processed: 536 average time/residue: 1.6871 time to fit residues: 1000.0252 Evaluate side-chains 408 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 402 time to evaluate : 2.530 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 3.2905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 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: 4.9990 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: 2.7588 ------------------------------------------------------------------------------- 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 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 141 ASN M 166 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 22551 Z= 0.230 Angle : 0.596 5.170 31033 Z= 0.331 Chirality : 0.045 0.156 3595 Planarity : 0.005 0.030 3826 Dihedral : 7.834 178.000 3672 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 2691 helix: 0.06 (0.13), residues: 1443 sheet: None (None), residues: 0 loop : 0.52 (0.17), residues: 1248 *********************** 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 459 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 428 time to evaluate : 2.588 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 442 average time/residue: 1.9799 time to fit residues: 955.7193 Evaluate side-chains 427 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 415 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 5 average time/residue: 1.1465 time to fit residues: 9.6617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 201 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 82 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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** 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: 0.8833 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22551 Z= 0.212 Angle : 0.557 5.105 31033 Z= 0.308 Chirality : 0.044 0.154 3595 Planarity : 0.004 0.029 3826 Dihedral : 7.625 176.985 3672 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.66 % 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: 1.00 (0.16), residues: 2691 helix: 0.83 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.69 (0.17), residues: 1248 *********************** 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 439 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 425 time to evaluate : 2.677 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 433 average time/residue: 2.1140 time to fit residues: 997.1393 Evaluate side-chains 420 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 413 time to evaluate : 2.537 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.0265 time to fit residues: 5.8069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 0.3980 chunk 242 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 126 optimal weight: 0.3980 chunk 230 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** 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: 0.8816 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 22551 Z= 0.184 Angle : 0.518 4.997 31033 Z= 0.287 Chirality : 0.042 0.149 3595 Planarity : 0.004 0.030 3826 Dihedral : 7.442 176.947 3672 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.16), residues: 2691 helix: 1.18 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.76 (0.18), residues: 1248 *********************** 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 447 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 430 time to evaluate : 2.530 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 438 average time/residue: 2.0906 time to fit residues: 999.9238 Evaluate side-chains 428 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 422 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.3532 time to fit residues: 3.8238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 3 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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** D 149 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 22551 Z= 0.385 Angle : 0.736 5.751 31033 Z= 0.407 Chirality : 0.052 0.182 3595 Planarity : 0.006 0.047 3826 Dihedral : 8.161 177.459 3672 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 2691 helix: 0.88 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.88 (0.18), residues: 1248 *********************** 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 450 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 430 time to evaluate : 2.499 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 444 average time/residue: 2.0079 time to fit residues: 972.2953 Evaluate side-chains 432 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 416 time to evaluate : 2.513 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 1.0409 time to fit residues: 9.2526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 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 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** F 142 ASN ** 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: 0.8856 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 22551 Z= 0.258 Angle : 0.611 5.113 31033 Z= 0.338 Chirality : 0.046 0.166 3595 Planarity : 0.005 0.031 3826 Dihedral : 7.825 176.856 3672 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.16), residues: 2691 helix: 1.06 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.92 (0.18), residues: 1248 *********************** 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 443 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 420 time to evaluate : 2.523 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 436 average time/residue: 2.1177 time to fit residues: 1004.6185 Evaluate side-chains 425 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 411 time to evaluate : 2.543 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.8123 time to fit residues: 5.2538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 187 optimal weight: 0.0970 chunk 145 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 overall best weight: 4.4184 ------------------------------------------------------------------------------- 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** F 142 ASN ** G 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8873 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 22551 Z= 0.315 Angle : 0.675 5.188 31033 Z= 0.374 Chirality : 0.049 0.177 3595 Planarity : 0.005 0.040 3826 Dihedral : 7.907 177.083 3672 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.03 % 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: 1.30 (0.16), residues: 2691 helix: 0.98 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.96 (0.18), residues: 1248 *********************** 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 443 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 421 time to evaluate : 2.690 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 437 average time/residue: 2.0549 time to fit residues: 978.5610 Evaluate side-chains 432 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 416 time to evaluate : 2.763 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.8475 time to fit residues: 6.6480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** F 142 ASN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 22551 Z= 0.201 Angle : 0.550 5.635 31033 Z= 0.305 Chirality : 0.043 0.155 3595 Planarity : 0.004 0.029 3826 Dihedral : 7.490 176.589 3672 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.16), residues: 2691 helix: 1.24 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.95 (0.18), residues: 1248 *********************** 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 440 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 420 time to evaluate : 2.762 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 436 average time/residue: 2.1335 time to fit residues: 1016.9035 Evaluate side-chains 431 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 417 time to evaluate : 2.624 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.4509 time to fit residues: 5.0533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 6.9990 chunk 245 optimal weight: 20.0000 chunk 224 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** F 142 ASN ** 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: 0.8828 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 22551 Z= 0.198 Angle : 0.541 5.019 31033 Z= 0.300 Chirality : 0.043 0.156 3595 Planarity : 0.004 0.029 3826 Dihedral : 7.408 176.735 3672 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.16), residues: 2691 helix: 1.31 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.97 (0.18), residues: 1248 *********************** 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 443 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 426 time to evaluate : 2.501 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 439 average time/residue: 2.0670 time to fit residues: 988.6093 Evaluate side-chains 432 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 419 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.3441 time to fit residues: 3.6740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 119 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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** F 142 ASN ** 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 106 ASN ** 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: 0.8840 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 22551 Z= 0.228 Angle : 0.574 5.861 31033 Z= 0.319 Chirality : 0.044 0.161 3595 Planarity : 0.004 0.029 3826 Dihedral : 7.520 176.994 3672 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.70 % 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: 1.57 (0.16), residues: 2691 helix: 1.28 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.98 (0.18), residues: 1248 ********************** 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 430 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 415 time to evaluate : 2.433 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 428 average time/residue: 2.0661 time to fit residues: 961.9216 Evaluate side-chains 428 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 415 time to evaluate : 2.562 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 1.6770 time to fit residues: 5.1093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 31 optimal weight: 0.0020 chunk 58 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 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: 4.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- 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** F 142 ASN ** 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 106 ASN ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.136034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116652 restraints weight = 18643.287| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 0.85 r_work: 0.3097 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22551 Z= 0.216 Angle : 0.561 5.775 31033 Z= 0.311 Chirality : 0.044 0.159 3595 Planarity : 0.004 0.029 3826 Dihedral : 7.481 176.891 3672 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.66 % 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: 1.60 (0.16), residues: 2691 helix: 1.31 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : 0.98 (0.18), residues: 1248 =============================================================================== Job complete usr+sys time: 12617.80 seconds wall clock time: 221 minutes 14.65 seconds (13274.65 seconds total)