Starting phenix.real_space_refine (version: dev) on Wed Dec 14 13:24:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/12_2022/6kfh_9973.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/12_2022/6kfh_9973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/12_2022/6kfh_9973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/12_2022/6kfh_9973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/12_2022/6kfh_9973.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/12_2022/6kfh_9973.pdb" } resolution = 3.6 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= 0.018 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 ASP 54": "OD1" <-> "OD2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 155": "OD1" <-> "OD2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ASP 153": "OD1" <-> "OD2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "G PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ASP 153": "OD1" <-> "OD2" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "H PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 20840 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 11.28, per 1000 atoms: 0.54 Number of scatterers: 20840 At special positions: 0 Unit cell: (124.432, 124.432, 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 3568 8.00 N 3344 7.00 C 13832 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: 8.65 Conformation dependent library (CDL) restraints added in 2.9 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 71.1% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.516A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (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 274 removed outlier: 4.039A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 337 through 350 removed outlier: 3.804A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.523A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 159' Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (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 274 removed outlier: 4.039A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE C 158 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 159' Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (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 274 removed outlier: 4.040A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 337 through 350 removed outlier: 3.802A pdb=" N ASP C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE D 158 " --> pdb=" O ASP D 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 159' Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 3.518A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (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 274 removed outlier: 4.039A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix Processing helix chain 'E' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE E 158 " --> pdb=" O ASP E 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 159' Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (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 274 removed outlier: 4.038A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 133 removed outlier: 4.549A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix Processing helix chain 'F' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 3.603A pdb=" N PHE F 158 " --> pdb=" O ASP F 155 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 155 through 159' Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (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 274 removed outlier: 4.039A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 334 Processing helix chain 'F' and resid 337 through 350 removed outlier: 3.802A pdb=" N ASP F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.523A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE G 158 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 155 through 159' Processing helix chain 'G' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (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 274 removed outlier: 4.039A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 334 Processing helix chain 'G' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE H 158 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 155 through 159' Processing helix chain 'H' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (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 274 removed outlier: 4.039A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 334 Processing helix chain 'H' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP H 343 " --> pdb=" O LEU H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA2, first strand: chain 'B' and resid 245 through 246 Processing sheet with id=AA3, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA4, first strand: chain 'D' and resid 245 through 246 Processing sheet with id=AA5, first strand: chain 'E' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'F' and resid 245 through 246 Processing sheet with id=AA7, first strand: chain 'G' and resid 245 through 246 Processing sheet with id=AA8, first strand: chain 'H' and resid 245 through 246 1224 hydrogen bonds defined for protein. 3648 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: 5.72 Time building geometry restraints manager: 9.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6232 1.34 - 1.46: 5580 1.46 - 1.58: 9524 1.58 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 21472 Sorted by residual: bond pdb=" CA ILE G 56 " pdb=" CB ILE G 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.94e+00 bond pdb=" CA ILE F 56 " pdb=" CB ILE F 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.85e+00 bond pdb=" CA ILE E 56 " pdb=" CB ILE E 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.71e+00 bond pdb=" CA ILE C 56 " pdb=" CB ILE C 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.63e+00 bond pdb=" CA ILE A 56 " pdb=" CB ILE A 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.59e+00 ... (remaining 21467 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.64: 464 106.64 - 113.50: 11740 113.50 - 120.36: 8728 120.36 - 127.21: 8004 127.21 - 134.07: 336 Bond angle restraints: 29272 Sorted by residual: angle pdb=" C TRP C 59 " pdb=" N THR C 60 " pdb=" CA THR C 60 " ideal model delta sigma weight residual 121.95 110.30 11.65 3.74e+00 7.15e-02 9.70e+00 angle pdb=" C TRP F 59 " pdb=" N THR F 60 " pdb=" CA THR F 60 " ideal model delta sigma weight residual 121.95 110.35 11.60 3.74e+00 7.15e-02 9.63e+00 angle pdb=" C TRP H 59 " pdb=" N THR H 60 " pdb=" CA THR H 60 " ideal model delta sigma weight residual 121.95 110.36 11.59 3.74e+00 7.15e-02 9.61e+00 angle pdb=" C TRP B 59 " pdb=" N THR B 60 " pdb=" CA THR B 60 " ideal model delta sigma weight residual 121.95 110.37 11.58 3.74e+00 7.15e-02 9.59e+00 angle pdb=" C TRP A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta sigma weight residual 121.95 110.37 11.58 3.74e+00 7.15e-02 9.58e+00 ... (remaining 29267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 10564 15.88 - 31.77: 1284 31.77 - 47.65: 360 47.65 - 63.53: 8 63.53 - 79.41: 24 Dihedral angle restraints: 12240 sinusoidal: 4704 harmonic: 7536 Sorted by residual: dihedral pdb=" CA ASP F 28 " pdb=" C ASP F 28 " pdb=" N ARG F 29 " pdb=" CA ARG F 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ASP C 28 " pdb=" C ASP C 28 " pdb=" N ARG C 29 " pdb=" CA ARG C 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ASP D 28 " pdb=" C ASP D 28 " pdb=" N ARG D 29 " pdb=" CA ARG D 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 12237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1979 0.036 - 0.071: 907 0.071 - 0.107: 237 0.107 - 0.143: 86 0.143 - 0.178: 23 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CA GLU G 274 " pdb=" N GLU G 274 " pdb=" C GLU G 274 " pdb=" CB GLU G 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA GLU D 274 " pdb=" N GLU D 274 " pdb=" C GLU D 274 " pdb=" CB GLU D 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA GLU F 274 " pdb=" N GLU F 274 " pdb=" C GLU F 274 " pdb=" CB GLU F 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3229 not shown) Planarity restraints: 3584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 305 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C LYS G 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS G 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR G 306 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 305 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS H 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS H 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR H 306 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 305 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS F 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS F 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR F 306 " 0.008 2.00e-02 2.50e+03 ... (remaining 3581 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5610 2.78 - 3.31: 20640 3.31 - 3.84: 33880 3.84 - 4.37: 37027 4.37 - 4.90: 64227 Nonbonded interactions: 161384 Sorted by model distance: nonbonded pdb=" O ASN F 31 " pdb=" OG1 THR F 35 " model vdw 2.255 2.440 nonbonded pdb=" O ASN E 31 " pdb=" OG1 THR E 35 " model vdw 2.255 2.440 nonbonded pdb=" O ASN G 31 " pdb=" OG1 THR G 35 " model vdw 2.255 2.440 nonbonded pdb=" O ASN D 31 " pdb=" OG1 THR D 35 " model vdw 2.255 2.440 nonbonded pdb=" O ASN B 31 " pdb=" OG1 THR B 35 " model vdw 2.255 2.440 ... (remaining 161379 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 13832 2.51 5 N 3344 2.21 5 O 3568 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.250 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.190 Process input model: 52.280 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.007 0.050 21472 Z= 0.449 Angle : 0.735 11.650 29272 Z= 0.389 Chirality : 0.045 0.178 3232 Planarity : 0.003 0.021 3584 Dihedral : 14.752 79.413 7312 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.15), residues: 2480 helix: -0.95 (0.11), residues: 1680 sheet: -5.11 (0.18), residues: 40 loop : -4.48 (0.16), residues: 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 2.353 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: 0 outliers final: 0 residues processed: 772 average time/residue: 0.3262 time to fit residues: 380.6194 Evaluate side-chains 510 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 2.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN A 232 GLN A 247 HIS A 270 ASN A 329 GLN B 199 GLN B 212 GLN B 232 GLN B 247 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN C 212 GLN C 232 GLN C 247 HIS C 329 GLN D 199 GLN D 212 GLN D 232 GLN D 247 HIS ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 329 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 232 GLN E 247 HIS ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 63 GLN F 212 GLN F 232 GLN F 247 HIS ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN G 50 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN G 232 GLN G 247 HIS ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN H 199 GLN H 212 GLN H 232 GLN H 247 HIS ** H 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 21472 Z= 0.204 Angle : 0.616 6.146 29272 Z= 0.320 Chirality : 0.042 0.161 3232 Planarity : 0.004 0.066 3584 Dihedral : 5.055 22.320 2752 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2480 helix: 0.20 (0.12), residues: 1696 sheet: None (None), residues: 0 loop : -4.02 (0.17), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 591 time to evaluate : 2.376 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 revert: symmetry clash outliers start: 58 outliers final: 45 residues processed: 627 average time/residue: 0.2919 time to fit residues: 286.9707 Evaluate side-chains 544 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 499 time to evaluate : 2.233 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.1902 time to fit residues: 18.8668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 0.0040 chunk 243 optimal weight: 0.4980 chunk 200 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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** A 270 ASN A 314 ASN A 329 GLN C 50 HIS C 329 GLN E 50 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN G 329 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 21472 Z= 0.156 Angle : 0.583 8.929 29272 Z= 0.299 Chirality : 0.041 0.180 3232 Planarity : 0.003 0.041 3584 Dihedral : 4.618 18.777 2752 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % 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: -0.80 (0.17), residues: 2480 helix: 0.76 (0.12), residues: 1720 sheet: None (None), residues: 0 loop : -3.71 (0.18), residues: 760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 636 time to evaluate : 2.366 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 16 residues processed: 661 average time/residue: 0.2951 time to fit residues: 305.9077 Evaluate side-chains 563 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 547 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2070 time to fit residues: 9.2004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 0.0050 chunk 151 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 21472 Z= 0.282 Angle : 0.632 10.870 29272 Z= 0.319 Chirality : 0.043 0.185 3232 Planarity : 0.003 0.043 3584 Dihedral : 4.718 20.441 2752 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2480 helix: 0.80 (0.12), residues: 1736 sheet: -4.09 (0.38), residues: 40 loop : -3.53 (0.20), residues: 704 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 536 time to evaluate : 2.368 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 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: 67 outliers final: 49 residues processed: 576 average time/residue: 0.2897 time to fit residues: 264.6494 Evaluate side-chains 558 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 509 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.1841 time to fit residues: 20.1041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 3 optimal weight: 0.0670 chunk 178 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 204 optimal weight: 8.9990 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- 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** A 270 ASN A 314 ASN ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 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** E 314 ASN F 50 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 21472 Z= 0.180 Angle : 0.588 8.254 29272 Z= 0.298 Chirality : 0.042 0.182 3232 Planarity : 0.003 0.043 3584 Dihedral : 4.573 21.925 2752 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 1.27 % 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: -0.42 (0.17), residues: 2480 helix: 1.06 (0.12), residues: 1720 sheet: -4.09 (0.40), residues: 40 loop : -3.50 (0.19), residues: 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 592 time to evaluate : 2.368 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 610 average time/residue: 0.2867 time to fit residues: 277.0614 Evaluate side-chains 531 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 519 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2228 time to fit residues: 7.7601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** A 270 ASN ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 21472 Z= 0.200 Angle : 0.622 11.431 29272 Z= 0.308 Chirality : 0.042 0.190 3232 Planarity : 0.003 0.044 3584 Dihedral : 4.505 19.909 2752 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 2.26 % 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: -0.26 (0.17), residues: 2480 helix: 1.19 (0.12), residues: 1720 sheet: -4.05 (0.43), residues: 40 loop : -3.45 (0.19), residues: 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 542 time to evaluate : 2.348 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 23 residues processed: 572 average time/residue: 0.2768 time to fit residues: 254.2142 Evaluate side-chains 540 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 517 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1824 time to fit residues: 11.2830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** A 270 ASN A 314 ASN A 329 GLN B 50 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8216 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 21472 Z= 0.358 Angle : 0.685 13.113 29272 Z= 0.344 Chirality : 0.046 0.206 3232 Planarity : 0.004 0.044 3584 Dihedral : 4.813 24.050 2752 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer Outliers : 2.49 % 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: -0.40 (0.17), residues: 2480 helix: 1.01 (0.12), residues: 1736 sheet: -3.76 (0.52), residues: 40 loop : -3.41 (0.20), residues: 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 538 time to evaluate : 2.292 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 revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 38 residues processed: 568 average time/residue: 0.2832 time to fit residues: 258.9296 Evaluate side-chains 549 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 511 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1817 time to fit residues: 16.2965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** A 314 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN E 329 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 21472 Z= 0.220 Angle : 0.654 13.608 29272 Z= 0.323 Chirality : 0.043 0.205 3232 Planarity : 0.003 0.049 3584 Dihedral : 4.665 26.402 2752 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 0.91 % 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: -0.22 (0.17), residues: 2480 helix: 1.19 (0.12), residues: 1720 sheet: -3.86 (0.50), residues: 40 loop : -3.37 (0.19), residues: 720 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 554 time to evaluate : 2.402 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 revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 563 average time/residue: 0.2885 time to fit residues: 258.5786 Evaluate side-chains 540 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 527 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1918 time to fit residues: 7.8690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 174 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 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** E 314 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 21472 Z= 0.163 Angle : 0.651 13.648 29272 Z= 0.318 Chirality : 0.042 0.195 3232 Planarity : 0.003 0.048 3584 Dihedral : 4.432 23.024 2752 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.59 % 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: -0.00 (0.17), residues: 2480 helix: 1.34 (0.12), residues: 1720 sheet: -4.09 (0.44), residues: 40 loop : -3.22 (0.20), residues: 720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 608 time to evaluate : 2.586 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: 13 outliers final: 10 residues processed: 613 average time/residue: 0.2804 time to fit residues: 275.0605 Evaluate side-chains 590 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 580 time to evaluate : 2.346 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1752 time to fit residues: 6.5472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 1.9990 chunk 143 optimal weight: 0.0030 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 156 optimal weight: 0.7980 overall best weight: 1.0794 ------------------------------------------------------------------------------- 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** A 314 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 21472 Z= 0.187 Angle : 0.682 13.386 29272 Z= 0.330 Chirality : 0.042 0.189 3232 Planarity : 0.003 0.049 3584 Dihedral : 4.422 22.095 2752 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.18 % 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 (0.17), residues: 2480 helix: 1.39 (0.12), residues: 1720 sheet: -3.83 (0.49), residues: 40 loop : -3.21 (0.20), residues: 720 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 595 time to evaluate : 2.363 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: 4 outliers final: 3 residues processed: 595 average time/residue: 0.3006 time to fit residues: 281.3077 Evaluate side-chains 568 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 565 time to evaluate : 2.349 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1969 time to fit residues: 4.2857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 173 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 70 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105585 restraints weight = 30247.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109461 restraints weight = 16600.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112035 restraints weight = 11185.894| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 21472 Z= 0.185 Angle : 0.687 13.303 29272 Z= 0.333 Chirality : 0.042 0.195 3232 Planarity : 0.004 0.049 3584 Dihedral : 4.409 20.894 2752 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 0.36 % 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: 0.07 (0.17), residues: 2480 helix: 1.38 (0.13), residues: 1728 sheet: -3.87 (0.47), residues: 40 loop : -3.21 (0.20), residues: 712 =============================================================================== Job complete usr+sys time: 4735.38 seconds wall clock time: 86 minutes 0.72 seconds (5160.72 seconds total)