Starting phenix.real_space_refine (version: dev) on Wed Dec 14 15:07:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/12_2022/6kff_9971.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/12_2022/6kff_9971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/12_2022/6kff_9971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/12_2022/6kff_9971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/12_2022/6kff_9971.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/12_2022/6kff_9971.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 175": "OD1" <-> "OD2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ASP 175": "OD1" <-> "OD2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F ASP 136": "OD1" <-> "OD2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ASP 175": "OD1" <-> "OD2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G ASP 136": "OD1" <-> "OD2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ASP 175": "OD1" <-> "OD2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H ASP 136": "OD1" <-> "OD2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ASP 175": "OD1" <-> "OD2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 21192 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 11.57, per 1000 atoms: 0.55 Number of scatterers: 21192 At special positions: 0 Unit cell: (121.968, 121.968, 108.416, 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 96 16.00 O 3592 8.00 N 3432 7.00 C 14072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 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: 8.09 Conformation dependent library (CDL) restraints added in 2.7 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 71.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 3.830A pdb=" N GLY A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 3.829A pdb=" N GLY B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 350 Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.537A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.829A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 276 through 305 removed outlier: 4.070A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 350 Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.537A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 53 removed outlier: 4.057A pdb=" N ARG D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix removed outlier: 3.830A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.915A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 350 Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix removed outlier: 3.829A pdb=" N GLY E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 4.146A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 305 " --> pdb=" O TYR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 350 Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 364 " --> pdb=" O SER E 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 4.479A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix removed outlier: 3.830A pdb=" N GLY F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.917A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS F 305 " --> pdb=" O TYR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN F 363 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 364 " --> pdb=" O SER F 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 4.479A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix removed outlier: 3.829A pdb=" N GLY G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 4.146A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 168 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 276 through 305 removed outlier: 4.070A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 305 " --> pdb=" O TYR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 308 No H-bonds generated for 'chain 'G' and resid 306 through 308' Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.548A pdb=" N PHE G 330 " --> pdb=" O SER G 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 350 Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG G 362 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN G 363 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 364 " --> pdb=" O SER G 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 53 removed outlier: 4.057A pdb=" N ARG H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix removed outlier: 3.829A pdb=" N GLY H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 305 " --> pdb=" O TYR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 308 No H-bonds generated for 'chain 'H' and resid 306 through 308' Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE H 330 " --> pdb=" O SER H 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE H 331 " --> pdb=" O ASP H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 350 Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG H 362 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN H 363 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE H 364 " --> pdb=" O SER H 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 57 Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 56 through 57 Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 57 1240 hydrogen bonds defined for protein. 3624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6312 1.34 - 1.46: 5601 1.46 - 1.58: 9791 1.58 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 21832 Sorted by residual: bond pdb=" C ARG G 168 " pdb=" N PRO G 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.17e-01 bond pdb=" C ARG H 168 " pdb=" N PRO H 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.07e-01 bond pdb=" C ARG D 168 " pdb=" N PRO D 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.06e-01 bond pdb=" C ARG E 168 " pdb=" N PRO E 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.74e-01 bond pdb=" C ARG A 168 " pdb=" N PRO A 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.66e-01 ... (remaining 21827 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.08: 534 107.08 - 113.82: 11986 113.82 - 120.56: 9341 120.56 - 127.30: 7556 127.30 - 134.04: 327 Bond angle restraints: 29744 Sorted by residual: angle pdb=" C TRP G 107 " pdb=" N VAL G 108 " pdb=" CA VAL G 108 " ideal model delta sigma weight residual 120.33 122.46 -2.13 8.00e-01 1.56e+00 7.06e+00 angle pdb=" C TRP B 107 " pdb=" N VAL B 108 " pdb=" CA VAL B 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 7.00e+00 angle pdb=" C TRP C 107 " pdb=" N VAL C 108 " pdb=" CA VAL C 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 6.99e+00 angle pdb=" C TRP F 107 " pdb=" N VAL F 108 " pdb=" CA VAL F 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 6.99e+00 angle pdb=" C TRP E 107 " pdb=" N VAL E 108 " pdb=" CA VAL E 108 " ideal model delta sigma weight residual 120.33 122.44 -2.11 8.00e-01 1.56e+00 6.93e+00 ... (remaining 29739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 10949 17.32 - 34.64: 1251 34.64 - 51.96: 224 51.96 - 69.28: 16 69.28 - 86.60: 40 Dihedral angle restraints: 12480 sinusoidal: 4840 harmonic: 7640 Sorted by residual: dihedral pdb=" CB CYS F 76 " pdb=" SG CYS F 76 " pdb=" SG CYS F 248 " pdb=" CB CYS F 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.02 -44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS G 76 " pdb=" SG CYS G 76 " pdb=" SG CYS G 248 " pdb=" CB CYS G 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.01 -44.01 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.00 -44.00 1 1.00e+01 1.00e-02 2.69e+01 ... (remaining 12477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1859 0.026 - 0.051: 855 0.051 - 0.077: 412 0.077 - 0.103: 108 0.103 - 0.129: 54 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CA TRP B 236 " pdb=" N TRP B 236 " pdb=" C TRP B 236 " pdb=" CB TRP B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA TRP G 236 " pdb=" N TRP G 236 " pdb=" C TRP G 236 " pdb=" CB TRP G 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA TRP F 236 " pdb=" N TRP F 236 " pdb=" C TRP F 236 " pdb=" CB TRP F 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 3285 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 119 " -0.010 2.00e-02 2.50e+03 9.91e-03 1.72e+00 pdb=" CG PHE D 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE D 119 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 119 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 119 " -0.010 2.00e-02 2.50e+03 9.75e-03 1.66e+00 pdb=" CG PHE F 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE F 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE F 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 119 " -0.009 2.00e-02 2.50e+03 9.75e-03 1.66e+00 pdb=" CG PHE C 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 119 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 119 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 119 " -0.002 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1164 2.73 - 3.27: 22887 3.27 - 3.81: 35035 3.81 - 4.36: 38025 4.36 - 4.90: 66422 Nonbonded interactions: 163533 Sorted by model distance: nonbonded pdb=" O ASN D 31 " pdb=" OG1 THR D 35 " model vdw 2.182 2.440 nonbonded pdb=" O ASN A 31 " pdb=" OG1 THR A 35 " model vdw 2.183 2.440 nonbonded pdb=" O ASN B 31 " pdb=" OG1 THR B 35 " model vdw 2.183 2.440 nonbonded pdb=" O ASN G 31 " pdb=" OG1 THR G 35 " model vdw 2.183 2.440 nonbonded pdb=" O ASN F 31 " pdb=" OG1 THR F 35 " model vdw 2.183 2.440 ... (remaining 163528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14072 2.51 5 N 3432 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.170 Process input model: 50.360 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.004 0.026 21832 Z= 0.230 Angle : 0.604 7.440 29744 Z= 0.321 Chirality : 0.038 0.129 3288 Planarity : 0.003 0.021 3632 Dihedral : 15.084 86.599 7472 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2496 helix: -0.50 (0.11), residues: 1672 sheet: -4.64 (0.29), residues: 80 loop : -4.12 (0.18), residues: 744 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 926 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 928 average time/residue: 0.3432 time to fit residues: 471.8810 Evaluate side-chains 722 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 716 time to evaluate : 2.565 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1769 time to fit residues: 5.4993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 50 HIS A 234 ASN A 247 HIS A 329 GLN B 21 GLN B 234 ASN B 247 HIS B 270 ASN B 329 GLN C 21 GLN C 206 GLN C 234 ASN C 247 HIS C 329 GLN D 21 GLN D 234 ASN D 247 HIS D 270 ASN D 329 GLN E 21 GLN E 50 HIS E 234 ASN E 247 HIS E 329 GLN F 21 GLN F 50 HIS F 234 ASN F 247 HIS F 329 GLN G 21 GLN G 234 ASN G 247 HIS G 329 GLN H 21 GLN H 50 HIS H 234 ASN H 247 HIS H 329 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 21832 Z= 0.260 Angle : 0.644 9.768 29744 Z= 0.313 Chirality : 0.041 0.177 3288 Planarity : 0.004 0.037 3632 Dihedral : 4.908 23.571 2792 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer Outliers : 4.83 % 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: -1.22 (0.17), residues: 2496 helix: 0.52 (0.12), residues: 1688 sheet: -4.32 (0.33), residues: 80 loop : -3.64 (0.21), residues: 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 765 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 78 residues processed: 812 average time/residue: 0.3425 time to fit residues: 421.6163 Evaluate side-chains 763 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 685 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.1851 time to fit residues: 30.2934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN D 50 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 329 GLN G 50 HIS G 115 GLN G 270 ASN H 115 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 21832 Z= 0.190 Angle : 0.595 7.875 29744 Z= 0.288 Chirality : 0.040 0.142 3288 Planarity : 0.003 0.032 3632 Dihedral : 4.626 22.335 2792 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2496 helix: 0.90 (0.13), residues: 1688 sheet: -3.95 (0.37), residues: 80 loop : -3.34 (0.22), residues: 728 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 769 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 784 average time/residue: 0.3102 time to fit residues: 376.6583 Evaluate side-chains 728 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 702 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1761 time to fit residues: 11.9335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 233 optimal weight: 0.0670 chunk 247 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 70 ASN C 206 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN E 67 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN G 70 ASN G 270 ASN H 115 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 21832 Z= 0.214 Angle : 0.587 7.604 29744 Z= 0.288 Chirality : 0.039 0.146 3288 Planarity : 0.003 0.034 3632 Dihedral : 4.566 22.567 2792 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2496 helix: 1.07 (0.13), residues: 1696 sheet: -3.86 (0.39), residues: 80 loop : -3.25 (0.22), residues: 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 741 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 70 residues processed: 783 average time/residue: 0.3167 time to fit residues: 380.6688 Evaluate side-chains 761 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 691 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.1832 time to fit residues: 27.5804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 184 optimal weight: 0.0570 chunk 102 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 67 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN G 67 GLN H 67 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 21832 Z= 0.194 Angle : 0.587 11.692 29744 Z= 0.284 Chirality : 0.039 0.192 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.413 21.920 2792 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2496 helix: 1.16 (0.13), residues: 1728 sheet: -3.96 (0.37), residues: 80 loop : -3.07 (0.23), residues: 688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 761 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 28 residues processed: 788 average time/residue: 0.2973 time to fit residues: 366.8690 Evaluate side-chains 740 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 712 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1985 time to fit residues: 13.4076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 81 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 21832 Z= 0.157 Angle : 0.585 12.502 29744 Z= 0.283 Chirality : 0.038 0.218 3288 Planarity : 0.003 0.035 3632 Dihedral : 4.285 22.809 2792 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2496 helix: 1.29 (0.13), residues: 1728 sheet: -4.06 (0.35), residues: 80 loop : -3.02 (0.22), residues: 688 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 756 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 35 residues processed: 771 average time/residue: 0.3096 time to fit residues: 368.6888 Evaluate side-chains 724 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 689 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1852 time to fit residues: 15.4381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21832 Z= 0.173 Angle : 0.604 12.913 29744 Z= 0.290 Chirality : 0.039 0.180 3288 Planarity : 0.004 0.033 3632 Dihedral : 4.229 23.280 2792 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 1.82 % 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: 0.03 (0.18), residues: 2496 helix: 1.34 (0.13), residues: 1728 sheet: -4.07 (0.35), residues: 80 loop : -2.99 (0.22), residues: 688 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 752 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 771 average time/residue: 0.3058 time to fit residues: 369.9190 Evaluate side-chains 709 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 686 time to evaluate : 2.528 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2055 time to fit residues: 12.2773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS H 67 GLN H 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21832 Z= 0.221 Angle : 0.626 12.378 29744 Z= 0.301 Chirality : 0.040 0.165 3288 Planarity : 0.004 0.033 3632 Dihedral : 4.315 23.581 2792 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2496 helix: 1.33 (0.13), residues: 1728 sheet: -4.26 (0.33), residues: 80 loop : -2.97 (0.22), residues: 688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 729 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 33 residues processed: 740 average time/residue: 0.3096 time to fit residues: 354.0814 Evaluate side-chains 738 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 705 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1780 time to fit residues: 14.6334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 206 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 21832 Z= 0.219 Angle : 0.629 12.597 29744 Z= 0.302 Chirality : 0.040 0.165 3288 Planarity : 0.004 0.032 3632 Dihedral : 4.312 24.296 2792 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2496 helix: 1.34 (0.13), residues: 1728 sheet: -4.22 (0.34), residues: 80 loop : -2.86 (0.22), residues: 688 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 719 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 724 average time/residue: 0.3134 time to fit residues: 350.4927 Evaluate side-chains 709 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 700 time to evaluate : 2.552 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1809 time to fit residues: 6.5362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.1980 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 255 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 50 HIS C 79 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 206 GLN ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 21832 Z= 0.180 Angle : 0.624 13.626 29744 Z= 0.300 Chirality : 0.039 0.190 3288 Planarity : 0.004 0.031 3632 Dihedral : 4.229 23.000 2792 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2496 helix: 1.38 (0.13), residues: 1728 sheet: -4.07 (0.36), residues: 80 loop : -2.77 (0.22), residues: 688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 724 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 728 average time/residue: 0.3079 time to fit residues: 347.5639 Evaluate side-chains 714 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 701 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1882 time to fit residues: 7.9294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108010 restraints weight = 31694.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.111887 restraints weight = 16853.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114544 restraints weight = 11129.744| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 21832 Z= 0.239 Angle : 0.638 13.043 29744 Z= 0.309 Chirality : 0.040 0.192 3288 Planarity : 0.004 0.033 3632 Dihedral : 4.327 23.318 2792 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.18), residues: 2496 helix: 1.36 (0.13), residues: 1728 sheet: -4.15 (0.35), residues: 80 loop : -2.74 (0.22), residues: 688 =============================================================================== Job complete usr+sys time: 5674.19 seconds wall clock time: 102 minutes 15.04 seconds (6135.04 seconds total)