Starting phenix.real_space_refine on Sat Mar 16 13:33:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/03_2024/3j8i_6179_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/03_2024/3j8i_6179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/03_2024/3j8i_6179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/03_2024/3j8i_6179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/03_2024/3j8i_6179_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/03_2024/3j8i_6179_updated.pdb" } resolution = 4.7 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 ------------------------------------------------------------------------------- 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= -0.009 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9320 2.51 5 N 2490 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 4": "OE1" <-> "OE2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 224": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "G TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 334": "OE1" <-> "OE2" Residue "G ARG 335": "NH1" <-> "NH2" Residue "G TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 364": "OE1" <-> "OE2" Residue "G ARG 372": "NH1" <-> "NH2" Residue "G PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "H GLU 224": "OE1" <-> "OE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "H GLU 334": "OE1" <-> "OE2" Residue "H ARG 335": "NH1" <-> "NH2" Residue "H TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 364": "OE1" <-> "OE2" Residue "H ARG 372": "NH1" <-> "NH2" Residue "H PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14800 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "F" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "H" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.05, per 1000 atoms: 0.54 Number of scatterers: 14800 At special positions: 0 Unit cell: (110.25, 86.1, 194.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2870 8.00 N 2490 7.00 C 9320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 3.6 seconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 15 sheets defined 33.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.653A pdb=" N PHE D 90 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 143 removed outlier: 4.118A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 143' Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.238A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 212 through 215 No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.530A pdb=" N MET D 227 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 230 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.757A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.790A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 No H-bonds generated for 'chain 'D' and resid 291 through 294' Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.522A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 361 through 364 No H-bonds generated for 'chain 'D' and resid 361 through 364' Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.551A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 371' Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'E' and resid 82 through 90 removed outlier: 3.570A pdb=" N PHE E 90 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 143 removed outlier: 4.065A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 143' Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.228A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 209 Processing helix chain 'E' and resid 212 through 215 No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 223 through 232 removed outlier: 3.541A pdb=" N MET E 227 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 229 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA E 230 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.717A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.811A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 No H-bonds generated for 'chain 'E' and resid 291 through 294' Processing helix chain 'E' and resid 309 through 320 removed outlier: 3.537A pdb=" N THR E 318 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 361 through 364 No H-bonds generated for 'chain 'E' and resid 361 through 364' Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.513A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 371' Processing helix chain 'F' and resid 57 through 60 No H-bonds generated for 'chain 'F' and resid 57 through 60' Processing helix chain 'F' and resid 82 through 90 removed outlier: 3.614A pdb=" N PHE F 90 " --> pdb=" O HIS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 143 removed outlier: 4.079A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 143' Processing helix chain 'F' and resid 182 through 195 removed outlier: 4.305A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 209 Processing helix chain 'F' and resid 212 through 215 No H-bonds generated for 'chain 'F' and resid 212 through 215' Processing helix chain 'F' and resid 223 through 232 removed outlier: 3.558A pdb=" N MET F 227 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA F 230 " --> pdb=" O MET F 227 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA F 231 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 262 removed outlier: 3.733A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 274 through 283 removed outlier: 3.851A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 282 " --> pdb=" O THR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 309 through 320 removed outlier: 3.609A pdb=" N THR F 318 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 347 Processing helix chain 'F' and resid 361 through 364 No H-bonds generated for 'chain 'F' and resid 361 through 364' Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.534A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 367 through 371' Processing helix chain 'G' and resid 57 through 60 No H-bonds generated for 'chain 'G' and resid 57 through 60' Processing helix chain 'G' and resid 82 through 90 removed outlier: 3.612A pdb=" N PHE G 90 " --> pdb=" O HIS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 143 removed outlier: 4.050A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 137 through 143' Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 195 removed outlier: 4.226A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 209 Processing helix chain 'G' and resid 212 through 215 No H-bonds generated for 'chain 'G' and resid 212 through 215' Processing helix chain 'G' and resid 223 through 232 removed outlier: 3.553A pdb=" N MET G 227 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 230 " --> pdb=" O MET G 227 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA G 231 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 262 removed outlier: 3.747A pdb=" N PHE G 255 " --> pdb=" O ASN G 252 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 274 through 283 removed outlier: 3.767A pdb=" N TYR G 279 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 295 Processing helix chain 'G' and resid 309 through 320 removed outlier: 3.570A pdb=" N THR G 318 " --> pdb=" O GLN G 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 320 " --> pdb=" O GLU G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 Processing helix chain 'G' and resid 361 through 364 No H-bonds generated for 'chain 'G' and resid 361 through 364' Processing helix chain 'G' and resid 367 through 371 removed outlier: 3.560A pdb=" N HIS G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 367 through 371' Processing helix chain 'H' and resid 57 through 60 No H-bonds generated for 'chain 'H' and resid 57 through 60' Processing helix chain 'H' and resid 82 through 90 removed outlier: 3.590A pdb=" N PHE H 90 " --> pdb=" O HIS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 126 Processing helix chain 'H' and resid 137 through 143 removed outlier: 4.079A pdb=" N SER H 141 " --> pdb=" O GLN H 137 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 137 through 143' Processing helix chain 'H' and resid 182 through 195 removed outlier: 4.229A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 209 Processing helix chain 'H' and resid 212 through 215 No H-bonds generated for 'chain 'H' and resid 212 through 215' Processing helix chain 'H' and resid 223 through 232 removed outlier: 3.523A pdb=" N MET H 227 " --> pdb=" O GLU H 224 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA H 230 " --> pdb=" O MET H 227 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA H 231 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 262 removed outlier: 3.736A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 274 through 283 removed outlier: 3.871A pdb=" N TYR H 279 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 294 No H-bonds generated for 'chain 'H' and resid 291 through 294' Processing helix chain 'H' and resid 309 through 320 removed outlier: 3.560A pdb=" N THR H 318 " --> pdb=" O GLN H 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 347 Processing helix chain 'H' and resid 361 through 364 No H-bonds generated for 'chain 'H' and resid 361 through 364' Processing helix chain 'H' and resid 367 through 371 removed outlier: 3.554A pdb=" N HIS H 371 " --> pdb=" O PRO H 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 367 through 371' Processing sheet with id= A, first strand: chain 'D' and resid 7 through 9 removed outlier: 3.861A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 16 through 19 Processing sheet with id= C, first strand: chain 'D' and resid 162 through 165 removed outlier: 3.631A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 7 through 9 removed outlier: 3.811A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 16 through 19 Processing sheet with id= F, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.629A pdb=" N VAL E 163 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 7 through 9 removed outlier: 3.855A pdb=" N TYR F 133 " --> pdb=" O THR F 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= I, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.608A pdb=" N VAL F 163 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 152 " --> pdb=" O VAL F 163 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 7 through 9 removed outlier: 3.858A pdb=" N TYR G 133 " --> pdb=" O THR G 103 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= L, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.649A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL G 152 " --> pdb=" O VAL G 163 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.838A pdb=" N TYR H 133 " --> pdb=" O THR H 103 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 16 through 19 Processing sheet with id= O, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.643A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4526 1.34 - 1.48: 4024 1.48 - 1.63: 6385 1.63 - 1.77: 21 1.77 - 1.91: 164 Bond restraints: 15120 Sorted by residual: bond pdb=" C LEU D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.331 1.383 -0.052 7.90e-03 1.60e+04 4.29e+01 bond pdb=" C LEU H 171 " pdb=" N PRO H 172 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.05e+01 bond pdb=" C LEU F 171 " pdb=" N PRO F 172 " ideal model delta sigma weight residual 1.331 1.379 -0.047 7.90e-03 1.60e+04 3.55e+01 bond pdb=" CA ILE E 250 " pdb=" C ILE E 250 " ideal model delta sigma weight residual 1.526 1.474 0.052 9.00e-03 1.23e+04 3.32e+01 bond pdb=" C LEU E 171 " pdb=" N PRO E 172 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.24e+01 ... (remaining 15115 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.87: 547 105.87 - 113.29: 7617 113.29 - 120.72: 6773 120.72 - 128.15: 5453 128.15 - 135.58: 125 Bond angle restraints: 20515 Sorted by residual: angle pdb=" C VAL F 129 " pdb=" N PRO F 130 " pdb=" CA PRO F 130 " ideal model delta sigma weight residual 119.19 126.79 -7.60 1.06e+00 8.90e-01 5.13e+01 angle pdb=" C ALA D 108 " pdb=" N PRO D 109 " pdb=" CA PRO D 109 " ideal model delta sigma weight residual 119.78 127.02 -7.24 1.03e+00 9.43e-01 4.94e+01 angle pdb=" N ALA G 138 " pdb=" CA ALA G 138 " pdb=" C ALA G 138 " ideal model delta sigma weight residual 111.28 118.53 -7.25 1.09e+00 8.42e-01 4.42e+01 angle pdb=" C ALA G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta sigma weight residual 119.78 126.55 -6.77 1.03e+00 9.43e-01 4.32e+01 angle pdb=" N ALA D 138 " pdb=" CA ALA D 138 " pdb=" C ALA D 138 " ideal model delta sigma weight residual 111.36 118.09 -6.73 1.09e+00 8.42e-01 3.81e+01 ... (remaining 20510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8650 35.49 - 70.97: 411 70.97 - 106.46: 34 106.46 - 141.94: 5 141.94 - 177.43: 5 Dihedral angle restraints: 9105 sinusoidal: 3685 harmonic: 5420 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.33 -177.32 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 9102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1407 0.093 - 0.185: 657 0.185 - 0.278: 181 0.278 - 0.370: 24 0.370 - 0.463: 6 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO E 243 " pdb=" N PRO E 243 " pdb=" C PRO E 243 " pdb=" CB PRO E 243 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA PRO F 243 " pdb=" N PRO F 243 " pdb=" C PRO F 243 " pdb=" CB PRO F 243 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CA PRO H 243 " pdb=" N PRO H 243 " pdb=" C PRO H 243 " pdb=" CB PRO H 243 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 2272 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 166 " -0.071 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR D 166 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 166 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 166 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR D 166 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 166 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D 166 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 166 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 166 " 0.061 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR E 166 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR E 166 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 166 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR E 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 166 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 166 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 166 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 166 " -0.060 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR H 166 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR H 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 166 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR H 166 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 166 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR H 166 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR H 166 " -0.027 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 801 2.68 - 3.24: 17004 3.24 - 3.79: 24798 3.79 - 4.35: 32535 4.35 - 4.90: 50182 Nonbonded interactions: 125320 Sorted by model distance: nonbonded pdb=" O SER F 350 " pdb=" N PHE F 352 " model vdw 2.125 2.520 nonbonded pdb=" O TYR H 362 " pdb=" O ALA H 365 " model vdw 2.131 3.040 nonbonded pdb=" O TYR F 362 " pdb=" O ALA F 365 " model vdw 2.140 3.040 nonbonded pdb=" O TYR G 362 " pdb=" O ALA G 365 " model vdw 2.154 3.040 nonbonded pdb=" O SER D 350 " pdb=" N PHE D 352 " model vdw 2.160 2.520 ... (remaining 125315 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.850 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 41.440 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.018 0.120 15120 Z= 1.168 Angle : 1.668 11.796 20515 Z= 1.105 Chirality : 0.109 0.463 2275 Planarity : 0.007 0.098 2630 Dihedral : 19.470 177.430 5635 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 76.17 Ramachandran Plot: Outliers : 6.06 % Allowed : 6.43 % Favored : 87.51 % Rotamer: Outliers : 14.53 % Allowed : 14.65 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.17), residues: 1865 helix: -0.26 (0.22), residues: 500 sheet: 0.08 (0.37), residues: 205 loop : -1.71 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.009 TRP G 356 HIS 0.004 0.001 HIS E 101 PHE 0.030 0.005 PHE G 375 TYR 0.071 0.009 TYR D 166 ARG 0.012 0.002 ARG E 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 60 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 ILE cc_start: 0.8806 (mt) cc_final: 0.8105 (mt) REVERT: D 82 MET cc_start: 0.8828 (ttt) cc_final: 0.8509 (ttm) REVERT: D 116 ARG cc_start: 0.6769 (mtp180) cc_final: 0.6181 (mtp-110) REVERT: D 147 ARG cc_start: 0.7676 (mpp-170) cc_final: 0.7265 (mpp-170) REVERT: D 371 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7148 (t-90) REVERT: D 373 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6278 (tmmt) outliers start: 46 outliers final: 19 residues processed: 96 average time/residue: 0.1655 time to fit residues: 18.8365 Evaluate side-chains 60 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 162 ASN F 296 ASN F 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15120 Z= 0.247 Angle : 0.889 9.233 20515 Z= 0.444 Chirality : 0.047 0.189 2275 Planarity : 0.006 0.038 2630 Dihedral : 8.674 115.694 2095 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 1.88 % Allowed : 10.99 % Favored : 87.13 % Rotamer: Outliers : 0.31 % Allowed : 9.12 % Favored : 90.57 % 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: -1.73 (0.19), residues: 1865 helix: -0.36 (0.21), residues: 595 sheet: 0.01 (0.38), residues: 215 loop : -1.93 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 340 HIS 0.009 0.002 HIS G 40 PHE 0.006 0.001 PHE D 200 TYR 0.035 0.002 TYR H 169 ARG 0.005 0.001 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 9 VAL cc_start: 0.7368 (t) cc_final: 0.6967 (t) REVERT: F 25 ASP cc_start: 0.8498 (m-30) cc_final: 0.8011 (p0) REVERT: F 116 ARG cc_start: 0.7053 (mtp180) cc_final: 0.6814 (mtp-110) REVERT: F 132 MET cc_start: 0.6408 (ppp) cc_final: 0.6178 (ppp) REVERT: F 147 ARG cc_start: 0.7928 (mpp-170) cc_final: 0.7245 (mpp-170) REVERT: F 223 PHE cc_start: 0.8136 (t80) cc_final: 0.7895 (t80) REVERT: F 305 MET cc_start: 0.8782 (tpp) cc_final: 0.8497 (tpp) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.1775 time to fit residues: 14.9451 Evaluate side-chains 44 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 149 optimal weight: 0.1980 chunk 166 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 overall best weight: 7.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15120 Z= 0.253 Angle : 0.817 7.986 20515 Z= 0.405 Chirality : 0.045 0.173 2275 Planarity : 0.005 0.046 2630 Dihedral : 7.419 88.031 2095 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.99 % Favored : 87.67 % Rotamer: Outliers : 0.31 % Allowed : 4.09 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.18), residues: 1865 helix: -0.83 (0.20), residues: 575 sheet: -0.82 (0.41), residues: 170 loop : -1.62 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 340 HIS 0.005 0.002 HIS F 275 PHE 0.016 0.002 PHE H 200 TYR 0.011 0.001 TYR D 53 ARG 0.002 0.001 ARG G 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 ASP cc_start: 0.8555 (m-30) cc_final: 0.8040 (p0) REVERT: F 269 MET cc_start: 0.7687 (mpp) cc_final: 0.7094 (mmp) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1620 time to fit residues: 11.1998 Evaluate side-chains 42 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 178 optimal weight: 0.0020 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15120 Z= 0.178 Angle : 0.764 9.063 20515 Z= 0.378 Chirality : 0.044 0.157 2275 Planarity : 0.006 0.089 2630 Dihedral : 6.640 63.130 2095 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.19 % Favored : 88.74 % Rotamer: Outliers : 0.63 % Allowed : 4.09 % Favored : 95.28 % 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: -1.95 (0.19), residues: 1865 helix: -0.91 (0.19), residues: 625 sheet: -0.94 (0.35), residues: 230 loop : -1.62 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 340 HIS 0.004 0.001 HIS H 161 PHE 0.005 0.001 PHE E 352 TYR 0.010 0.001 TYR G 166 ARG 0.016 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 105 LEU cc_start: 0.7882 (mm) cc_final: 0.7488 (tp) REVERT: F 211 ASP cc_start: 0.8068 (p0) cc_final: 0.7016 (t0) REVERT: F 217 CYS cc_start: 0.7487 (p) cc_final: 0.7022 (m) REVERT: F 269 MET cc_start: 0.8170 (mpp) cc_final: 0.7877 (mmm) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.1422 time to fit residues: 10.0657 Evaluate side-chains 44 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 30.0000 chunk 101 optimal weight: 30.0000 chunk 2 optimal weight: 0.0770 chunk 133 optimal weight: 0.0980 chunk 73 optimal weight: 0.2980 chunk 152 optimal weight: 40.0000 chunk 123 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 0.0270 chunk 160 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 overall best weight: 0.1134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN F 173 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15120 Z= 0.181 Angle : 0.768 7.326 20515 Z= 0.377 Chirality : 0.045 0.151 2275 Planarity : 0.006 0.063 2630 Dihedral : 6.438 58.113 2095 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.65 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -1.90 (0.19), residues: 1865 helix: -0.86 (0.20), residues: 585 sheet: -0.90 (0.33), residues: 230 loop : -1.58 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 79 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE D 31 TYR 0.016 0.001 TYR G 306 ARG 0.008 0.001 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 105 LEU cc_start: 0.7760 (mm) cc_final: 0.7531 (tp) REVERT: F 132 MET cc_start: 0.6376 (ppp) cc_final: 0.6060 (tmm) REVERT: F 269 MET cc_start: 0.7866 (mpp) cc_final: 0.7293 (mmp) REVERT: F 284 LYS cc_start: 0.8321 (mmpt) cc_final: 0.7879 (tttt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1062 time to fit residues: 7.1561 Evaluate side-chains 42 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 chunk 59 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15120 Z= 0.167 Angle : 0.725 10.732 20515 Z= 0.357 Chirality : 0.042 0.145 2275 Planarity : 0.006 0.072 2630 Dihedral : 5.783 36.332 2095 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 1.34 % Allowed : 9.65 % Favored : 89.01 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -1.90 (0.18), residues: 1865 helix: -0.80 (0.20), residues: 600 sheet: -0.67 (0.34), residues: 220 loop : -1.70 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 79 HIS 0.002 0.001 HIS G 161 PHE 0.009 0.001 PHE D 31 TYR 0.008 0.001 TYR G 166 ARG 0.008 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 132 MET cc_start: 0.6729 (ppp) cc_final: 0.6237 (tmm) REVERT: F 269 MET cc_start: 0.8163 (mpp) cc_final: 0.7876 (mmm) REVERT: F 305 MET cc_start: 0.8786 (mmt) cc_final: 0.8553 (mmt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1206 time to fit residues: 7.7669 Evaluate side-chains 41 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 130 optimal weight: 0.0370 chunk 150 optimal weight: 6.9990 chunk 99 optimal weight: 0.0970 chunk 178 optimal weight: 5.9990 chunk 111 optimal weight: 30.0000 chunk 108 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 3.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15120 Z= 0.172 Angle : 0.756 8.234 20515 Z= 0.367 Chirality : 0.043 0.161 2275 Planarity : 0.005 0.064 2630 Dihedral : 5.613 33.286 2095 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.65 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -2.01 (0.18), residues: 1865 helix: -0.93 (0.20), residues: 605 sheet: -0.98 (0.35), residues: 205 loop : -1.66 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 86 HIS 0.008 0.001 HIS G 161 PHE 0.009 0.001 PHE F 31 TYR 0.007 0.001 TYR E 166 ARG 0.009 0.001 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6154 (mmp) cc_final: 0.3604 (mtm) REVERT: F 105 LEU cc_start: 0.8075 (mm) cc_final: 0.7741 (tp) REVERT: F 269 MET cc_start: 0.8258 (mpp) cc_final: 0.7945 (mmm) REVERT: F 299 MET cc_start: 0.8717 (ptm) cc_final: 0.8355 (ppp) REVERT: F 306 TYR cc_start: 0.7507 (m-80) cc_final: 0.7258 (m-10) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1279 time to fit residues: 7.9726 Evaluate side-chains 40 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 20.0000 chunk 106 optimal weight: 0.1980 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 88 optimal weight: 0.0010 chunk 16 optimal weight: 50.0000 chunk 140 optimal weight: 20.0000 chunk 162 optimal weight: 0.7980 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15120 Z= 0.179 Angle : 0.738 6.965 20515 Z= 0.362 Chirality : 0.044 0.276 2275 Planarity : 0.005 0.053 2630 Dihedral : 5.557 36.312 2095 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 1.07 % Allowed : 10.19 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -2.05 (0.18), residues: 1865 helix: -0.94 (0.20), residues: 610 sheet: -0.93 (0.34), residues: 205 loop : -1.72 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 86 HIS 0.002 0.000 HIS E 161 PHE 0.008 0.001 PHE D 31 TYR 0.009 0.001 TYR H 166 ARG 0.008 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6134 (mmp) cc_final: 0.3550 (mtm) REVERT: F 105 LEU cc_start: 0.8067 (mm) cc_final: 0.7804 (tp) REVERT: F 269 MET cc_start: 0.8310 (mpp) cc_final: 0.7974 (mmm) REVERT: F 284 LYS cc_start: 0.8297 (mmpt) cc_final: 0.7862 (tttt) REVERT: F 299 MET cc_start: 0.8690 (ptm) cc_final: 0.8418 (ppp) REVERT: F 306 TYR cc_start: 0.7364 (m-80) cc_final: 0.7144 (m-10) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1413 time to fit residues: 7.8418 Evaluate side-chains 38 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 chunk 166 optimal weight: 8.9990 chunk 100 optimal weight: 0.0770 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 3.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.7341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15120 Z= 0.176 Angle : 0.781 12.459 20515 Z= 0.379 Chirality : 0.044 0.249 2275 Planarity : 0.005 0.037 2630 Dihedral : 5.417 40.704 2095 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.38 % Favored : 89.54 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -2.01 (0.18), residues: 1865 helix: -0.92 (0.19), residues: 625 sheet: -1.09 (0.33), residues: 210 loop : -1.65 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 86 HIS 0.003 0.001 HIS E 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR E 166 ARG 0.008 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6317 (mmp) cc_final: 0.3770 (mtm) REVERT: F 105 LEU cc_start: 0.8038 (mm) cc_final: 0.7782 (tp) REVERT: F 269 MET cc_start: 0.8325 (mpp) cc_final: 0.7985 (mmm) REVERT: F 306 TYR cc_start: 0.7404 (m-80) cc_final: 0.7115 (m-10) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1424 time to fit residues: 7.9126 Evaluate side-chains 39 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 0.0870 chunk 184 optimal weight: 0.0980 chunk 169 optimal weight: 0.9990 chunk 146 optimal weight: 0.0870 chunk 15 optimal weight: 0.0670 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 0.0670 chunk 116 optimal weight: 20.0000 overall best weight: 0.0812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15120 Z= 0.159 Angle : 0.775 11.940 20515 Z= 0.371 Chirality : 0.044 0.261 2275 Planarity : 0.005 0.039 2630 Dihedral : 5.228 38.880 2095 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.65 % Favored : 89.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.96 (0.18), residues: 1865 helix: -0.76 (0.21), residues: 605 sheet: -0.84 (0.37), residues: 195 loop : -1.74 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 86 HIS 0.001 0.000 HIS G 173 PHE 0.005 0.001 PHE E 31 TYR 0.009 0.001 TYR G 166 ARG 0.003 0.000 ARG H 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 MET cc_start: 0.6135 (mmp) cc_final: 0.3703 (mtm) REVERT: F 72 GLU cc_start: 0.8052 (tt0) cc_final: 0.7790 (mt-10) REVERT: F 132 MET cc_start: 0.6466 (ppp) cc_final: 0.5633 (tmm) REVERT: F 269 MET cc_start: 0.8093 (mpp) cc_final: 0.7504 (mmp) REVERT: F 305 MET cc_start: 0.7200 (mmp) cc_final: 0.6954 (mmm) REVERT: F 316 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8365 (tp30) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1271 time to fit residues: 7.7426 Evaluate side-chains 39 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 135 optimal weight: 0.0770 chunk 21 optimal weight: 0.0470 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 129 optimal weight: 0.0970 overall best weight: 0.2212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.072994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066005 restraints weight = 15232.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.067410 restraints weight = 9698.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068446 restraints weight = 6700.354| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.7934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15120 Z= 0.155 Angle : 0.765 8.691 20515 Z= 0.359 Chirality : 0.044 0.260 2275 Planarity : 0.005 0.041 2630 Dihedral : 5.205 38.610 2095 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.80 % Allowed : 9.38 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -1.91 (0.18), residues: 1865 helix: -0.61 (0.21), residues: 590 sheet: -0.14 (0.34), residues: 245 loop : -2.01 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 86 HIS 0.001 0.000 HIS F 88 PHE 0.006 0.001 PHE G 31 TYR 0.008 0.001 TYR G 166 ARG 0.004 0.000 ARG F 147 =============================================================================== Job complete usr+sys time: 1890.63 seconds wall clock time: 35 minutes 57.76 seconds (2157.76 seconds total)