Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 15:51:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/10_2023/7vda_31912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/10_2023/7vda_31912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/10_2023/7vda_31912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/10_2023/7vda_31912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/10_2023/7vda_31912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/10_2023/7vda_31912.pdb" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 14736 2.51 5 N 4074 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "C PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "E PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F GLU 402": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 23292 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Time building chain proxies: 11.68, per 1000 atoms: 0.50 Number of scatterers: 23292 At special positions: 0 Unit cell: (109.85, 117.65, 156.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4368 8.00 N 4074 7.00 C 14736 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: 8.73 Conformation dependent library (CDL) restraints added in 3.6 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 58.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL A 198 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL A 317 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.605A pdb=" N VAL A 339 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 421 Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 100 through 118 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.529A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.947A pdb=" N VAL B 317 " --> pdb=" O ILE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.607A pdb=" N VAL B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 421 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 removed outlier: 4.852A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 100 through 118 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.947A pdb=" N VAL C 317 " --> pdb=" O ILE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL C 339 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 398 through 421 Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.740A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 Processing helix chain 'D' and resid 100 through 118 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.529A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.573A pdb=" N PHE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL D 317 " --> pdb=" O ILE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL D 339 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 398 through 421 Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 53 Processing helix chain 'E' and resid 100 through 118 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 186 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL E 317 " --> pdb=" O ILE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL E 339 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 363 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 398 through 421 Processing helix chain 'E' and resid 433 through 442 Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 53 Processing helix chain 'F' and resid 100 through 118 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 186 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.573A pdb=" N PHE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL F 317 " --> pdb=" O ILE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 363 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'F' and resid 375 through 391 Processing helix chain 'F' and resid 398 through 421 Processing helix chain 'F' and resid 433 through 442 Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.740A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA F 480 " --> pdb=" O ASP F 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.547A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 3.670A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE A 247 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY A 274 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 249 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 322 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.548A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 273 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE B 247 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY B 274 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 249 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 322 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.548A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 273 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE C 247 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY C 274 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 249 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 322 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE D 247 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLY D 274 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 249 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 322 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 273 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE E 247 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY E 274 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 249 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 322 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL F 273 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE F 247 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLY F 274 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL F 249 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU F 322 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) 1374 hydrogen bonds defined for protein. 3924 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: 8.14 Time building geometry restraints manager: 9.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7746 1.35 - 1.46: 5388 1.46 - 1.58: 10464 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 23790 Sorted by residual: bond pdb=" CB LYS A 342 " pdb=" CG LYS A 342 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CB LYS B 342 " pdb=" CG LYS B 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB LYS C 342 " pdb=" CG LYS C 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB LYS D 342 " pdb=" CG LYS D 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB LYS F 342 " pdb=" CG LYS F 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 23785 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.59: 438 105.59 - 112.68: 12441 112.68 - 119.78: 7761 119.78 - 126.88: 11220 126.88 - 133.97: 258 Bond angle restraints: 32118 Sorted by residual: angle pdb=" CB MET E 233 " pdb=" CG MET E 233 " pdb=" SD MET E 233 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET A 233 " pdb=" CG MET A 233 " pdb=" SD MET A 233 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET B 233 " pdb=" CG MET B 233 " pdb=" SD MET B 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET C 233 " pdb=" CG MET C 233 " pdb=" SD MET C 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET F 233 " pdb=" CG MET F 233 " pdb=" SD MET F 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.11e+01 ... (remaining 32113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 12196 17.78 - 35.55: 1460 35.55 - 53.33: 468 53.33 - 71.11: 90 71.11 - 88.88: 48 Dihedral angle restraints: 14262 sinusoidal: 5784 harmonic: 8478 Sorted by residual: dihedral pdb=" CA LYS D 420 " pdb=" C LYS D 420 " pdb=" N PHE D 421 " pdb=" CA PHE D 421 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LYS B 420 " pdb=" C LYS B 420 " pdb=" N PHE B 421 " pdb=" CA PHE B 421 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LYS E 420 " pdb=" C LYS E 420 " pdb=" N PHE E 421 " pdb=" CA PHE E 421 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 14259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2138 0.028 - 0.056: 821 0.056 - 0.084: 311 0.084 - 0.111: 157 0.111 - 0.139: 65 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CA ILE D 280 " pdb=" N ILE D 280 " pdb=" C ILE D 280 " pdb=" CB ILE D 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 280 " pdb=" N ILE B 280 " pdb=" C ILE B 280 " pdb=" CB ILE B 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 280 " pdb=" N ILE C 280 " pdb=" C ILE C 280 " pdb=" CB ILE C 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3489 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 282 " -0.035 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO D 283 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 283 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 283 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 282 " 0.035 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 283 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 282 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO B 283 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " 0.030 5.00e-02 4.00e+02 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 425 2.69 - 3.25: 22597 3.25 - 3.80: 38986 3.80 - 4.35: 51149 4.35 - 4.90: 85292 Nonbonded interactions: 198449 Sorted by model distance: nonbonded pdb=" OG1 THR F 272 " pdb=" O ILE F 280 " model vdw 2.142 2.440 nonbonded pdb=" OG1 THR A 272 " pdb=" O ILE A 280 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR B 272 " pdb=" O ILE B 280 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR E 272 " pdb=" O ILE E 280 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR C 272 " pdb=" O ILE C 280 " model vdw 2.143 2.440 ... (remaining 198444 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.210 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: 0.030 Extract box with map and model: 15.210 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 59.030 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.003 0.034 23790 Z= 0.166 Angle : 0.531 10.055 32118 Z= 0.296 Chirality : 0.041 0.139 3492 Planarity : 0.004 0.054 4182 Dihedral : 17.671 88.884 8862 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.20 % Allowed : 19.15 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.67 (0.16), residues: 2964 helix: 2.57 (0.13), residues: 1542 sheet: -0.25 (0.28), residues: 396 loop : -0.63 (0.19), residues: 1026 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 323 time to evaluate : 2.742 Fit side-chains outliers start: 55 outliers final: 48 residues processed: 362 average time/residue: 1.5144 time to fit residues: 620.1912 Evaluate side-chains 337 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 289 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 10 average time/residue: 0.2915 time to fit residues: 8.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 463 GLN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN C 374 ASN C 463 GLN ** D 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 463 GLN ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN F 374 ASN F 463 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23790 Z= 0.331 Angle : 0.651 7.602 32118 Z= 0.350 Chirality : 0.048 0.145 3492 Planarity : 0.006 0.065 4182 Dihedral : 4.903 20.036 3258 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 7.41 % Allowed : 15.50 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.85 (0.15), residues: 2964 helix: 1.84 (0.13), residues: 1584 sheet: -0.37 (0.26), residues: 396 loop : -1.13 (0.19), residues: 984 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 322 time to evaluate : 2.742 Fit side-chains outliers start: 185 outliers final: 92 residues processed: 448 average time/residue: 1.3731 time to fit residues: 703.7477 Evaluate side-chains 410 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 318 time to evaluate : 2.729 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 71 residues processed: 25 average time/residue: 0.5837 time to fit residues: 22.8755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 330 GLN A 414 GLN B 254 ASN B 374 ASN B 463 GLN C 330 GLN C 374 ASN D 254 ASN E 254 ASN E 374 ASN E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23790 Z= 0.255 Angle : 0.579 7.436 32118 Z= 0.313 Chirality : 0.045 0.136 3492 Planarity : 0.005 0.046 4182 Dihedral : 4.707 19.009 3258 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 7.05 % Allowed : 16.27 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.83 (0.15), residues: 2964 helix: 1.89 (0.13), residues: 1584 sheet: -0.40 (0.26), residues: 396 loop : -1.27 (0.18), residues: 984 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 313 time to evaluate : 2.672 Fit side-chains outliers start: 176 outliers final: 111 residues processed: 422 average time/residue: 1.4153 time to fit residues: 682.1232 Evaluate side-chains 421 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 310 time to evaluate : 2.849 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 85 residues processed: 30 average time/residue: 0.7637 time to fit residues: 33.0383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 179 optimal weight: 0.0670 chunk 268 optimal weight: 20.0000 chunk 284 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN A 374 ASN B 297 GLN B 374 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN E 297 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23790 Z= 0.194 Angle : 0.521 6.786 32118 Z= 0.283 Chirality : 0.043 0.133 3492 Planarity : 0.004 0.038 4182 Dihedral : 4.475 18.131 3258 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.49 % Allowed : 17.31 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.99 (0.15), residues: 2964 helix: 2.11 (0.13), residues: 1584 sheet: -0.50 (0.26), residues: 396 loop : -1.29 (0.18), residues: 984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 303 time to evaluate : 3.419 Fit side-chains outliers start: 162 outliers final: 100 residues processed: 414 average time/residue: 1.3625 time to fit residues: 646.1113 Evaluate side-chains 395 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 295 time to evaluate : 2.867 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 76 residues processed: 28 average time/residue: 0.5226 time to fit residues: 23.9264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 4 optimal weight: 0.2980 chunk 211 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23790 Z= 0.350 Angle : 0.653 8.246 32118 Z= 0.354 Chirality : 0.049 0.152 3492 Planarity : 0.006 0.069 4182 Dihedral : 4.972 20.002 3258 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.53 % Allowed : 17.71 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.50 (0.15), residues: 2964 helix: 1.66 (0.13), residues: 1584 sheet: -0.35 (0.27), residues: 396 loop : -1.61 (0.18), residues: 984 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 317 time to evaluate : 2.722 Fit side-chains outliers start: 163 outliers final: 104 residues processed: 424 average time/residue: 1.3721 time to fit residues: 667.5702 Evaluate side-chains 422 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 318 time to evaluate : 2.723 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 78 residues processed: 30 average time/residue: 0.7057 time to fit residues: 30.8104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 0.3980 chunk 70 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 374 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23790 Z= 0.168 Angle : 0.509 7.137 32118 Z= 0.275 Chirality : 0.043 0.131 3492 Planarity : 0.004 0.037 4182 Dihedral : 4.375 17.607 3258 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.01 % Allowed : 18.95 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.99 (0.15), residues: 2964 helix: 2.15 (0.13), residues: 1584 sheet: -0.33 (0.26), residues: 384 loop : -1.45 (0.18), residues: 996 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 306 time to evaluate : 3.112 Fit side-chains outliers start: 125 outliers final: 86 residues processed: 395 average time/residue: 1.4321 time to fit residues: 646.5368 Evaluate side-chains 385 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 299 time to evaluate : 2.741 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 66 residues processed: 22 average time/residue: 0.6174 time to fit residues: 21.2984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 162 optimal weight: 0.0970 chunk 207 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 177 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23790 Z= 0.126 Angle : 0.462 9.731 32118 Z= 0.248 Chirality : 0.041 0.126 3492 Planarity : 0.004 0.033 4182 Dihedral : 3.979 15.714 3258 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.93 % Allowed : 21.03 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.36 (0.16), residues: 2964 helix: 2.56 (0.13), residues: 1548 sheet: -0.43 (0.26), residues: 384 loop : -1.24 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 312 time to evaluate : 2.759 Fit side-chains outliers start: 98 outliers final: 64 residues processed: 385 average time/residue: 1.4009 time to fit residues: 615.5288 Evaluate side-chains 353 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 289 time to evaluate : 2.548 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 56 residues processed: 8 average time/residue: 0.2461 time to fit residues: 6.9028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 180 optimal weight: 0.0270 chunk 193 optimal weight: 2.9990 chunk 140 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 374 ASN B 254 ASN B 297 GLN B 374 ASN B 414 GLN B 463 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN D 414 GLN E 254 ASN E 374 ASN E 414 GLN E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23790 Z= 0.124 Angle : 0.466 9.948 32118 Z= 0.247 Chirality : 0.041 0.133 3492 Planarity : 0.004 0.033 4182 Dihedral : 3.868 15.384 3258 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.17 % Allowed : 21.63 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.42 (0.16), residues: 2964 helix: 2.60 (0.13), residues: 1548 sheet: -0.44 (0.26), residues: 384 loop : -1.17 (0.18), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 307 time to evaluate : 2.917 Fit side-chains outliers start: 79 outliers final: 57 residues processed: 370 average time/residue: 1.4271 time to fit residues: 601.8245 Evaluate side-chains 342 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 285 time to evaluate : 2.576 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 50 residues processed: 7 average time/residue: 0.6956 time to fit residues: 9.6056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 8.9990 chunk 271 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 254 ASN B 463 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 374 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN E 254 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 374 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23790 Z= 0.176 Angle : 0.517 8.946 32118 Z= 0.275 Chirality : 0.043 0.135 3492 Planarity : 0.004 0.040 4182 Dihedral : 4.149 17.513 3258 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.41 % Allowed : 21.55 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.22 (0.16), residues: 2964 helix: 2.35 (0.13), residues: 1584 sheet: -0.68 (0.26), residues: 414 loop : -1.16 (0.18), residues: 966 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 303 time to evaluate : 2.720 Fit side-chains outliers start: 85 outliers final: 66 residues processed: 365 average time/residue: 1.4409 time to fit residues: 601.7249 Evaluate side-chains 361 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 295 time to evaluate : 2.853 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 51 residues processed: 16 average time/residue: 0.8104 time to fit residues: 19.8655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 374 ASN B 254 ASN B 374 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN E 254 ASN E 374 ASN F 254 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23790 Z= 0.227 Angle : 0.572 9.025 32118 Z= 0.305 Chirality : 0.045 0.140 3492 Planarity : 0.005 0.044 4182 Dihedral : 4.452 18.624 3258 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.12 % Allowed : 21.79 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.94 (0.16), residues: 2964 helix: 2.09 (0.13), residues: 1584 sheet: -0.81 (0.26), residues: 426 loop : -1.21 (0.18), residues: 954 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 302 time to evaluate : 2.772 Fit side-chains outliers start: 78 outliers final: 69 residues processed: 360 average time/residue: 1.3452 time to fit residues: 556.8825 Evaluate side-chains 362 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 293 time to evaluate : 2.849 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 52 residues processed: 19 average time/residue: 0.6730 time to fit residues: 20.2876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 254 ASN B 374 ASN B 463 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 374 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN E 254 ASN E 374 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 374 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137245 restraints weight = 24476.005| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.39 r_work: 0.3432 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23790 Z= 0.148 Angle : 0.503 8.712 32118 Z= 0.268 Chirality : 0.042 0.141 3492 Planarity : 0.004 0.040 4182 Dihedral : 4.116 16.674 3258 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.68 % Allowed : 22.28 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.12 (0.16), residues: 2964 helix: 2.31 (0.13), residues: 1572 sheet: -0.36 (0.26), residues: 384 loop : -1.42 (0.18), residues: 1008 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10386.86 seconds wall clock time: 184 minutes 44.21 seconds (11084.21 seconds total)