Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 02:57:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/04_2023/7usy_26743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/04_2023/7usy_26743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/04_2023/7usy_26743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/04_2023/7usy_26743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/04_2023/7usy_26743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usy_26743/04_2023/7usy_26743_updated.pdb" } resolution = 3.54 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 4 5.49 5 S 95 5.16 5 C 10812 2.51 5 N 2770 2.21 5 O 2893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "J GLU 180": "OE1" <-> "OE2" Residue "J GLU 256": "OE1" <-> "OE2" Residue "J GLU 317": "OE1" <-> "OE2" Residue "J ARG 337": "NH1" <-> "NH2" Residue "J GLU 383": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16582 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4864 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 18, 'TRANS': 583} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4864 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 18, 'TRANS': 583} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2878 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' CA': 2, '3PE': 1, 'NAG': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {' CA': 2, '3PE': 1, 'NAG': 1, 'PEE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 9.00, per 1000 atoms: 0.54 Number of scatterers: 16582 At special positions: 0 Unit cell: (143.469, 119.138, 156.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 95 16.00 P 4 15.00 O 2893 8.00 N 2770 7.00 C 10812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 816 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 2.4 seconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 10 sheets defined 56.2% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 4.642A pdb=" N ARG A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 120 removed outlier: 4.330A pdb=" N SER A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 148 removed outlier: 3.539A pdb=" N TYR A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 168 through 190 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 205 through 215 removed outlier: 5.126A pdb=" N THR A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.996A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 262 through 289 removed outlier: 3.608A pdb=" N PHE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 319 through 342 Processing helix chain 'A' and resid 350 through 380 removed outlier: 3.625A pdb=" N CYS A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 416 removed outlier: 3.536A pdb=" N VAL A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Proline residue: A 407 - end of helix removed outlier: 3.688A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 458 Processing helix chain 'A' and resid 668 through 694 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 725 through 743 Processing helix chain 'A' and resid 749 through 771 removed outlier: 3.791A pdb=" N ILE A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 809 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 825 through 836 removed outlier: 3.853A pdb=" N VAL A 828 " --> pdb=" O PHE A 825 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG A 831 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 834 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 835 " --> pdb=" O GLU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 849 removed outlier: 3.693A pdb=" N HIS A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 879 Proline residue: A 856 - end of helix Processing helix chain 'B' and resid 76 through 93 Processing helix chain 'B' and resid 100 through 120 removed outlier: 4.490A pdb=" N SER B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 148 Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.821A pdb=" N PHE B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 205 through 215 removed outlier: 5.116A pdb=" N THR B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.093A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 262 through 289 removed outlier: 3.760A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 319 through 342 Processing helix chain 'B' and resid 350 through 380 Processing helix chain 'B' and resid 392 through 416 removed outlier: 4.444A pdb=" N VAL B 395 " --> pdb=" O LYS B 392 " (cutoff:3.500A) Proline residue: B 396 - end of helix removed outlier: 4.057A pdb=" N VAL B 399 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 400 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) Proline residue: B 407 - end of helix Processing helix chain 'B' and resid 421 through 458 Processing helix chain 'B' and resid 668 through 694 Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 725 through 742 Processing helix chain 'B' and resid 749 through 770 removed outlier: 3.783A pdb=" N ILE B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 809 Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 826 through 833 removed outlier: 4.109A pdb=" N ARG B 831 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 849 removed outlier: 3.578A pdb=" N HIS B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 849 " --> pdb=" O ILE B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 879 Proline residue: B 856 - end of helix Processing helix chain 'C' and resid 22 through 31 Processing helix chain 'C' and resid 36 through 49 Processing helix chain 'C' and resid 62 through 65 No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.676A pdb=" N SER C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 196 No H-bonds generated for 'chain 'C' and resid 193 through 196' Processing helix chain 'D' and resid 24 through 45 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 65 No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 139 through 150 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 180 through 189 removed outlier: 4.905A pdb=" N ARG E 189 " --> pdb=" O HIS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 196 No H-bonds generated for 'chain 'E' and resid 193 through 196' Processing helix chain 'F' and resid 24 through 45 removed outlier: 3.704A pdb=" N PHE F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'J' and resid 180 through 183 No H-bonds generated for 'chain 'J' and resid 180 through 183' Processing helix chain 'J' and resid 363 through 365 No H-bonds generated for 'chain 'J' and resid 363 through 365' Processing sheet with id= A, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= B, first strand: chain 'E' and resid 67 through 69 Processing sheet with id= C, first strand: chain 'J' and resid 120 through 129 Processing sheet with id= D, first strand: chain 'J' and resid 85 through 94 removed outlier: 3.658A pdb=" N GLY J 65 " --> pdb=" O ASP J 155 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR J 148 " --> pdb=" O PHE J 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 186 through 193 Processing sheet with id= F, first strand: chain 'J' and resid 214 through 216 removed outlier: 6.365A pdb=" N THR J 330 " --> pdb=" O TYR J 215 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'J' and resid 256 through 258 removed outlier: 3.710A pdb=" N GLU J 256 " --> pdb=" O VAL J 249 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR J 308 " --> pdb=" O LEU J 329 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 347 through 350 Processing sheet with id= I, first strand: chain 'J' and resid 65 through 72 removed outlier: 6.401A pdb=" N VAL J 68 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU J 101 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU J 70 " --> pdb=" O LYS J 99 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS J 99 " --> pdb=" O LEU J 70 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLY J 72 " --> pdb=" O ASP J 97 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP J 97 " --> pdb=" O GLY J 72 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 238 through 244 removed outlier: 3.622A pdb=" N PHE J 265 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN J 243 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL J 263 " --> pdb=" O GLN J 243 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2547 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: 4.31 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2562 1.31 - 1.44: 4665 1.44 - 1.56: 9560 1.56 - 1.69: 9 1.69 - 1.82: 152 Bond restraints: 16948 Sorted by residual: bond pdb=" C21 3PE B1304 " pdb=" O21 3PE B1304 " ideal model delta sigma weight residual 1.316 1.399 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C21 3PE A1304 " pdb=" O21 3PE A1304 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C30 PEE B1303 " pdb=" O3 PEE B1303 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C30 PEE A1303 " pdb=" O3 PEE A1303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C31 3PE A1304 " pdb=" O31 3PE A1304 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 16943 not shown) Histogram of bond angle deviations from ideal: 92.55 - 100.92: 42 100.92 - 109.30: 1072 109.30 - 117.67: 11461 117.67 - 126.05: 10085 126.05 - 134.42: 245 Bond angle restraints: 22905 Sorted by residual: angle pdb=" C ASN J 340 " pdb=" N ALA J 341 " pdb=" CA ALA J 341 " ideal model delta sigma weight residual 120.68 133.70 -13.02 1.52e+00 4.33e-01 7.34e+01 angle pdb=" N SER A 870 " pdb=" CA SER A 870 " pdb=" C SER A 870 " ideal model delta sigma weight residual 111.14 102.17 8.97 1.08e+00 8.57e-01 6.90e+01 angle pdb=" C MET A 810 " pdb=" N SER A 811 " pdb=" CA SER A 811 " ideal model delta sigma weight residual 121.61 132.79 -11.18 1.39e+00 5.18e-01 6.47e+01 angle pdb=" C GLN B 301 " pdb=" CA GLN B 301 " pdb=" CB GLN B 301 " ideal model delta sigma weight residual 116.54 109.86 6.68 1.15e+00 7.56e-01 3.37e+01 angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 109.74 -16.83 3.00e+00 1.11e-01 3.15e+01 ... (remaining 22900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 9211 24.40 - 48.80: 843 48.80 - 73.19: 65 73.19 - 97.59: 10 97.59 - 121.99: 1 Dihedral angle restraints: 10130 sinusoidal: 4163 harmonic: 5967 Sorted by residual: dihedral pdb=" CA PRO J 344 " pdb=" C PRO J 344 " pdb=" N PRO J 345 " pdb=" CA PRO J 345 " ideal model delta harmonic sigma weight residual 180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA VAL A 395 " pdb=" C VAL A 395 " pdb=" N PRO A 396 " pdb=" CA PRO A 396 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C12 PEE A1303 " pdb=" C10 PEE A1303 " pdb=" C11 PEE A1303 " pdb=" O4 PEE A1303 " ideal model delta sinusoidal sigma weight residual -19.47 -141.46 121.99 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 10127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1798 0.038 - 0.076: 609 0.076 - 0.115: 149 0.115 - 0.153: 21 0.153 - 0.191: 3 Chirality restraints: 2580 Sorted by residual: chirality pdb=" C2 PEE A1303 " pdb=" C1 PEE A1303 " pdb=" C3 PEE A1303 " pdb=" O2 PEE A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CG LEU F 30 " pdb=" CB LEU F 30 " pdb=" CD1 LEU F 30 " pdb=" CD2 LEU F 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ILE J 338 " pdb=" N ILE J 338 " pdb=" C ILE J 338 " pdb=" CB ILE J 338 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 2577 not shown) Planarity restraints: 2843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.202 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" C7 NAG B1305 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.272 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.115 2.00e-02 2.50e+03 9.50e-02 1.13e+02 pdb=" C7 NAG A1305 " -0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.151 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 395 " 0.087 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 396 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.070 5.00e-02 4.00e+02 ... (remaining 2840 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 4 2.11 - 2.81: 4507 2.81 - 3.51: 23201 3.51 - 4.20: 35105 4.20 - 4.90: 64811 Nonbonded interactions: 127628 Sorted by model distance: nonbonded pdb=" OD1 ASP C 171 " pdb="CA CA C 302 " model vdw 1.415 2.510 nonbonded pdb=" ND2 ASN A 209 " pdb=" C3 NAG A1305 " model vdw 1.424 3.550 nonbonded pdb=" ND2 ASN B 209 " pdb=" C3 NAG B1305 " model vdw 1.467 3.550 nonbonded pdb=" OE1 GLU C 182 " pdb="CA CA C 302 " model vdw 1.981 2.510 nonbonded pdb=" OE2 GLU C 182 " pdb="CA CA C 302 " model vdw 2.124 2.510 ... (remaining 127623 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' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.620 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: 14.710 Check model and map are aligned: 0.280 Set scattering table: 0.140 Process input model: 41.640 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 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 0.083 16948 Z= 0.253 Angle : 0.778 16.825 22905 Z= 0.402 Chirality : 0.041 0.191 2580 Planarity : 0.006 0.167 2843 Dihedral : 16.476 121.990 6256 Min Nonbonded Distance : 1.415 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.55 (0.19), residues: 2005 helix: 2.08 (0.15), residues: 1157 sheet: 0.95 (0.38), residues: 169 loop : -0.83 (0.24), residues: 679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 180 average time/residue: 0.3135 time to fit residues: 84.4332 Evaluate side-chains 161 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1471 time to fit residues: 3.3516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 95 optimal weight: 0.4980 chunk 116 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 879 ASN C 57 ASN J 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 16948 Z= 0.152 Angle : 0.502 7.690 22905 Z= 0.254 Chirality : 0.040 0.255 2580 Planarity : 0.004 0.063 2843 Dihedral : 6.812 95.639 2352 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.78 (0.19), residues: 2005 helix: 2.24 (0.15), residues: 1161 sheet: 1.15 (0.39), residues: 169 loop : -0.74 (0.24), residues: 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 169 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 18 residues processed: 202 average time/residue: 0.2817 time to fit residues: 88.1125 Evaluate side-chains 173 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1583 time to fit residues: 8.1924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 731 HIS B 420 HIS B 674 GLN B 735 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 16948 Z= 0.326 Angle : 0.612 9.795 22905 Z= 0.314 Chirality : 0.044 0.169 2580 Planarity : 0.005 0.065 2843 Dihedral : 6.946 78.259 2352 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.31 (0.19), residues: 2005 helix: 1.80 (0.15), residues: 1146 sheet: 1.27 (0.39), residues: 169 loop : -0.83 (0.24), residues: 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 178 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 35 residues processed: 237 average time/residue: 0.2727 time to fit residues: 99.5723 Evaluate side-chains 199 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.890 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1618 time to fit residues: 13.0335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 193 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 181 ASN B 420 HIS B 735 ASN B 736 GLN B 879 ASN C 59 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16948 Z= 0.183 Angle : 0.499 9.566 22905 Z= 0.256 Chirality : 0.040 0.151 2580 Planarity : 0.004 0.054 2843 Dihedral : 6.629 66.003 2352 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 2005 helix: 2.09 (0.15), residues: 1143 sheet: 1.31 (0.40), residues: 169 loop : -0.81 (0.24), residues: 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 200 average time/residue: 0.2737 time to fit residues: 85.9581 Evaluate side-chains 182 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1594 time to fit residues: 8.0629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 0.2980 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 98 optimal weight: 0.6980 chunk 173 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS C 59 GLN J 267 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16948 Z= 0.198 Angle : 0.507 8.612 22905 Z= 0.260 Chirality : 0.040 0.161 2580 Planarity : 0.004 0.052 2843 Dihedral : 6.461 55.991 2352 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.58 (0.19), residues: 2005 helix: 2.06 (0.15), residues: 1144 sheet: 1.37 (0.40), residues: 169 loop : -0.79 (0.24), residues: 692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 22 residues processed: 203 average time/residue: 0.2732 time to fit residues: 86.1413 Evaluate side-chains 188 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1534 time to fit residues: 9.0109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 193 optimal weight: 0.0030 chunk 160 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16948 Z= 0.139 Angle : 0.474 8.435 22905 Z= 0.241 Chirality : 0.039 0.158 2580 Planarity : 0.004 0.052 2843 Dihedral : 6.189 56.688 2352 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.77 (0.19), residues: 2005 helix: 2.24 (0.15), residues: 1152 sheet: 1.34 (0.39), residues: 169 loop : -0.75 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 183 average time/residue: 0.2858 time to fit residues: 80.8457 Evaluate side-chains 168 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 2.114 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1594 time to fit residues: 4.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16948 Z= 0.181 Angle : 0.506 16.618 22905 Z= 0.255 Chirality : 0.040 0.158 2580 Planarity : 0.004 0.052 2843 Dihedral : 6.149 57.246 2352 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2005 helix: 2.11 (0.15), residues: 1153 sheet: 1.40 (0.40), residues: 169 loop : -0.73 (0.24), residues: 683 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 182 average time/residue: 0.2888 time to fit residues: 81.4529 Evaluate side-chains 171 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1708 time to fit residues: 5.0513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 420 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16948 Z= 0.176 Angle : 0.498 12.444 22905 Z= 0.253 Chirality : 0.040 0.161 2580 Planarity : 0.004 0.052 2843 Dihedral : 6.119 58.395 2352 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.70 (0.19), residues: 2005 helix: 2.15 (0.15), residues: 1149 sheet: 1.45 (0.40), residues: 169 loop : -0.75 (0.24), residues: 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 1.872 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 182 average time/residue: 0.2695 time to fit residues: 76.6710 Evaluate side-chains 169 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 1.952 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1631 time to fit residues: 4.5202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 78 optimal weight: 0.0040 chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 169 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16948 Z= 0.247 Angle : 0.554 12.441 22905 Z= 0.280 Chirality : 0.041 0.161 2580 Planarity : 0.004 0.051 2843 Dihedral : 6.314 58.099 2352 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.47 (0.19), residues: 2005 helix: 1.94 (0.15), residues: 1146 sheet: 1.49 (0.40), residues: 169 loop : -0.82 (0.24), residues: 690 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 2.173 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 178 average time/residue: 0.2806 time to fit residues: 78.5944 Evaluate side-chains 172 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1787 time to fit residues: 3.8548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 183 optimal weight: 40.0000 chunk 158 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 169 optimal weight: 30.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16948 Z= 0.182 Angle : 0.513 12.003 22905 Z= 0.260 Chirality : 0.040 0.161 2580 Planarity : 0.004 0.051 2843 Dihedral : 6.180 58.118 2352 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.65 (0.19), residues: 2005 helix: 2.11 (0.15), residues: 1146 sheet: 1.49 (0.41), residues: 169 loop : -0.78 (0.24), residues: 690 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.2863 time to fit residues: 77.9152 Evaluate side-chains 166 residues out of total 1819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1596 time to fit residues: 3.1229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.262991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.258895 restraints weight = 19988.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.238861 restraints weight = 44267.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.236074 restraints weight = 47275.314| |-----------------------------------------------------------------------------| r_work (final): 0.4846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16948 Z= 0.197 Angle : 0.524 11.904 22905 Z= 0.265 Chirality : 0.040 0.159 2580 Planarity : 0.004 0.052 2843 Dihedral : 6.153 58.890 2352 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 1.63 (0.19), residues: 2005 helix: 2.07 (0.15), residues: 1148 sheet: 1.50 (0.41), residues: 169 loop : -0.77 (0.24), residues: 688 =============================================================================== Job complete usr+sys time: 2828.87 seconds wall clock time: 52 minutes 46.02 seconds (3166.02 seconds total)