Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 14:13:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/04_2023/7tjq_25929.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/04_2023/7tjq_25929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/04_2023/7tjq_25929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/04_2023/7tjq_25929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/04_2023/7tjq_25929.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/04_2023/7tjq_25929.pdb" } resolution = 3.13 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 Anisotropic ADP refinement not supported. Converting 9645 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12867 2.51 5 N 3516 2.21 5 O 4026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20538 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3265 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3265 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3265 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "N" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "O" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.45, per 1000 atoms: 0.51 Number of scatterers: 20538 At special positions: 0 Unit cell: (162.81, 148.23, 106.11, 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 129 16.00 O 4026 8.00 N 3516 7.00 C 12867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 100B" distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 463 " distance=2.02 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 100B" distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 407 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 311 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 326 " - pdb=" SG CYS F 335 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 365 " - pdb=" SG CYS F 463 " distance=2.02 Simple disulfide: pdb=" SG CYS F 384 " - pdb=" SG CYS F 390 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 407 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 182 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 322 " distance=2.03 Simple disulfide: pdb=" SG CYS G 127 " - pdb=" SG CYS G 153 " distance=2.04 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 283 " - pdb=" SG CYS G 311 " distance=2.03 Simple disulfide: pdb=" SG CYS G 292 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 326 " - pdb=" SG CYS G 335 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 365 " - pdb=" SG CYS G 463 " distance=2.02 Simple disulfide: pdb=" SG CYS G 384 " - pdb=" SG CYS G 390 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.04 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 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG P 1 " - " ASN A 96 " " NAG Q 1 " - " ASN C 172 " " NAG R 1 " - " ASN D 96 " " NAG S 1 " - " ASN F 172 " " NAG T 1 " - " ASN G 172 " " NAG U 1 " - " ASN H 96 " Time building additional restraints: 8.35 Conformation dependent library (CDL) restraints added in 2.9 seconds 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4902 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 55 sheets defined 21.4% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.740A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.030A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 65 through 84 removed outlier: 3.512A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 129 removed outlier: 3.714A pdb=" N ILE C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 186 through 197 removed outlier: 4.164A pdb=" N ALA C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.658A pdb=" N ARG C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 460 through 463 No H-bonds generated for 'chain 'C' and resid 460 through 463' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.701A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'F' and resid 54 through 58 Processing helix chain 'F' and resid 65 through 84 Processing helix chain 'F' and resid 104 through 129 removed outlier: 3.862A pdb=" N ILE F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 186 through 197 removed outlier: 4.189A pdb=" N ALA F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 210 Processing helix chain 'F' and resid 223 through 234 removed outlier: 3.763A pdb=" N ARG F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 247 Processing helix chain 'F' and resid 247 through 255 Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 344 through 352 Processing helix chain 'F' and resid 441 through 446 Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'G' and resid 65 through 84 removed outlier: 3.606A pdb=" N THR G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 129 removed outlier: 3.777A pdb=" N ILE G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 163 through 172 Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 178 through 181 Processing helix chain 'G' and resid 187 through 197 Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 223 through 234 Processing helix chain 'G' and resid 237 through 247 Processing helix chain 'G' and resid 247 through 255 Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 344 through 347 Processing helix chain 'G' and resid 348 through 353 Processing helix chain 'G' and resid 441 through 446 Processing helix chain 'G' and resid 460 through 463 No H-bonds generated for 'chain 'G' and resid 460 through 463' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.679A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.540A pdb=" N ASP A 10 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.540A pdb=" N ASP A 10 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR A 100D" --> pdb=" O SER A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.185A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.948A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.826A pdb=" N GLY C 34 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS C 283 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 36 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR C 281 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 38 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE C 279 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP C 309 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR C 317 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AA9, first strand: chain 'C' and resid 146 through 150 removed outlier: 9.400A pdb=" N TRP C 43 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N LEU C 158 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR C 45 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR C 160 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 47 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL C 162 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR C 49 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 291 through 294 removed outlier: 7.009A pdb=" N CYS C 365 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE C 456 " --> pdb=" O CYS C 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AB3, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.909A pdb=" N ILE C 392 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLN C 402 " --> pdb=" O CYS C 390 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N CYS C 390 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 447 through 448 removed outlier: 4.412A pdb=" N ASP C 447 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.672A pdb=" N ASP D 10 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.672A pdb=" N ASP D 10 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR D 100D" --> pdb=" O SER D 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.570A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.988A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 327 through 329 removed outlier: 3.901A pdb=" N GLY F 34 " --> pdb=" O CYS F 283 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS F 283 " --> pdb=" O GLY F 34 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 36 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR F 281 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL F 38 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE F 279 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP F 309 " --> pdb=" O TYR F 320 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR F 317 " --> pdb=" O VAL F 343 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 327 through 329 removed outlier: 6.349A pdb=" N GLU F 21 " --> pdb=" O HIS F 435 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE F 437 " --> pdb=" O GLU F 21 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR F 23 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 150 removed outlier: 8.285A pdb=" N ARG F 156 " --> pdb=" O TRP F 43 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR F 45 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET F 270 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU F 259 " --> pdb=" O MET F 270 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN F 272 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLY F 257 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY F 257 " --> pdb=" O THR F 214 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 291 through 295 removed outlier: 6.956A pdb=" N CYS F 365 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE F 456 " --> pdb=" O CYS F 365 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 372 through 376 Processing sheet with id=AC7, first strand: chain 'F' and resid 398 through 402 removed outlier: 6.940A pdb=" N ILE F 392 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN F 402 " --> pdb=" O CYS F 390 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N CYS F 390 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 327 through 329 removed outlier: 4.006A pdb=" N GLY G 34 " --> pdb=" O CYS G 283 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS G 283 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU G 36 " --> pdb=" O THR G 281 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N THR G 281 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL G 38 " --> pdb=" O ILE G 279 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE G 279 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TRP G 309 " --> pdb=" O TYR G 320 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR G 317 " --> pdb=" O VAL G 343 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 327 through 329 removed outlier: 3.503A pdb=" N SER G 29 " --> pdb=" O LEU G 24 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 146 through 150 removed outlier: 9.388A pdb=" N TRP G 43 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N LEU G 158 " --> pdb=" O TRP G 43 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR G 45 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR G 160 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL G 47 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL G 162 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR G 49 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER G 266 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL G 262 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE G 268 " --> pdb=" O ILE G 260 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 257 " --> pdb=" O THR G 214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 291 through 294 removed outlier: 7.064A pdb=" N CYS G 365 " --> pdb=" O PHE G 456 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE G 456 " --> pdb=" O CYS G 365 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 372 through 376 Processing sheet with id=AD4, first strand: chain 'G' and resid 398 through 402 removed outlier: 6.945A pdb=" N ILE G 392 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLN G 402 " --> pdb=" O CYS G 390 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS G 390 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 447 through 448 removed outlier: 4.615A pdb=" N ASP G 447 " --> pdb=" O GLU G 465 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.528A pdb=" N ASP H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.528A pdb=" N ASP H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR H 100D" --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.012A pdb=" N SER I 33 " --> pdb=" O ALA I 99 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.076A pdb=" N CYS I 96 " --> pdb=" O TRP I 114 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP I 114 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG I 98 " --> pdb=" O ASP I 112 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.810A pdb=" N SER J 33 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 7.054A pdb=" N CYS J 96 " --> pdb=" O TRP J 114 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TRP J 114 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG J 98 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.494A pdb=" N VAL K 10 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.494A pdb=" N VAL K 10 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.961A pdb=" N GLY L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.472A pdb=" N VAL M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.472A pdb=" N VAL M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF5, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AF6, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.840A pdb=" N SER N 33 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.027A pdb=" N CYS N 96 " --> pdb=" O TRP N 114 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP N 114 " --> pdb=" O CYS N 96 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG N 98 " --> pdb=" O ASP N 112 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.436A pdb=" N VAL O 10 " --> pdb=" O THR O 108 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.436A pdb=" N VAL O 10 " --> pdb=" O THR O 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 18 through 23 1058 hydrogen bonds defined for protein. 2604 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: 9.90 Time building geometry restraints manager: 8.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6688 1.35 - 1.47: 5186 1.47 - 1.59: 8892 1.59 - 1.71: 0 1.71 - 1.83: 162 Bond restraints: 20928 Sorted by residual: bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.21e+00 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 20923 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.70: 498 106.70 - 113.60: 11540 113.60 - 120.50: 7668 120.50 - 127.40: 8497 127.40 - 134.30: 183 Bond angle restraints: 28386 Sorted by residual: angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 122.06 -8.16 1.80e+00 3.09e-01 2.05e+01 angle pdb=" C ASP O 52 " pdb=" N ASN O 53 " pdb=" CA ASN O 53 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 angle pdb=" CA TYR E 49 " pdb=" CB TYR E 49 " pdb=" CG TYR E 49 " ideal model delta sigma weight residual 113.90 120.25 -6.35 1.80e+00 3.09e-01 1.24e+01 angle pdb=" CA TYR K 51 " pdb=" CB TYR K 51 " pdb=" CG TYR K 51 " ideal model delta sigma weight residual 113.90 119.98 -6.08 1.80e+00 3.09e-01 1.14e+01 angle pdb=" C ASP M 52 " pdb=" N ASN M 53 " pdb=" CA ASN M 53 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 ... (remaining 28381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11639 17.97 - 35.93: 658 35.93 - 53.90: 141 53.90 - 71.87: 54 71.87 - 89.83: 18 Dihedral angle restraints: 12510 sinusoidal: 4830 harmonic: 7680 Sorted by residual: dihedral pdb=" CA ASN A 96 " pdb=" C ASN A 96 " pdb=" N CYS A 97 " pdb=" CA CYS A 97 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN D 96 " pdb=" C ASN D 96 " pdb=" N CYS D 97 " pdb=" CA CYS D 97 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASN H 96 " pdb=" C ASN H 96 " pdb=" N CYS H 97 " pdb=" CA CYS H 97 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 12507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2328 0.049 - 0.099: 780 0.099 - 0.148: 132 0.148 - 0.197: 17 0.197 - 0.247: 4 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 172 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN G 172 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA TYR L 49 " pdb=" N TYR L 49 " pdb=" C TYR L 49 " pdb=" CB TYR L 49 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3258 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 163 " 0.242 9.50e-02 1.11e+02 1.09e-01 9.39e+00 pdb=" NE ARG C 163 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 163 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 163 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 163 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 163 " 0.235 9.50e-02 1.11e+02 1.06e-01 8.77e+00 pdb=" NE ARG G 163 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG G 163 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG G 163 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG G 163 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 163 " 0.223 9.50e-02 1.11e+02 1.01e-01 7.94e+00 pdb=" NE ARG F 163 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG F 163 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG F 163 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 163 " 0.000 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5235 2.81 - 3.33: 19234 3.33 - 3.86: 35070 3.86 - 4.38: 42135 4.38 - 4.90: 73425 Nonbonded interactions: 175099 Sorted by model distance: nonbonded pdb=" OG1 THR I 102 " pdb=" OD2 ASP M 52 " model vdw 2.288 2.440 nonbonded pdb=" ND2 ASN C 412 " pdb=" O VAL C 430 " model vdw 2.336 2.520 nonbonded pdb=" O GLN F 307 " pdb=" OH TYR F 319 " model vdw 2.338 2.440 nonbonded pdb=" OG1 THR N 102 " pdb=" OD2 ASP O 52 " model vdw 2.343 2.440 nonbonded pdb=" OE2 GLU L 50 " pdb=" OH TYR L 91 " model vdw 2.344 2.440 ... (remaining 175094 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 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 19.330 Check model and map are aligned: 0.360 Set scattering table: 0.170 Process input model: 54.500 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 0.050 20928 Z= 0.281 Angle : 0.771 8.157 28386 Z= 0.442 Chirality : 0.049 0.247 3261 Planarity : 0.008 0.109 3618 Dihedral : 13.251 89.834 7464 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.55 (0.16), residues: 2643 helix: -0.72 (0.22), residues: 414 sheet: -0.19 (0.17), residues: 936 loop : -0.22 (0.17), residues: 1293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 604 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 621 average time/residue: 0.3681 time to fit residues: 333.1348 Evaluate side-chains 533 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 526 time to evaluate : 2.081 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1833 time to fit residues: 5.3286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 124 optimal weight: 0.0670 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 206 GLN F 307 GLN F 342 ASN G 195 GLN G 272 GLN G 298 ASN G 342 ASN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 20928 Z= 0.427 Angle : 0.704 9.513 28386 Z= 0.385 Chirality : 0.049 0.223 3261 Planarity : 0.005 0.048 3618 Dihedral : 5.761 24.711 2910 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.30 (0.16), residues: 2643 helix: 0.11 (0.24), residues: 420 sheet: -0.15 (0.17), residues: 903 loop : -0.19 (0.17), residues: 1320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 533 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 34 residues processed: 556 average time/residue: 0.3708 time to fit residues: 302.0833 Evaluate side-chains 545 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 511 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2361 time to fit residues: 16.9459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 161 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 190 optimal weight: 0.0970 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN E 92 ASN F 195 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN G 139 ASN G 202 ASN G 346 GLN G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 20928 Z= 0.272 Angle : 0.599 9.200 28386 Z= 0.323 Chirality : 0.045 0.169 3261 Planarity : 0.004 0.044 3618 Dihedral : 5.185 24.160 2910 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.13 (0.16), residues: 2643 helix: 0.34 (0.24), residues: 420 sheet: -0.10 (0.17), residues: 882 loop : -0.07 (0.17), residues: 1341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 505 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 522 average time/residue: 0.4029 time to fit residues: 307.6935 Evaluate side-chains 507 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 493 time to evaluate : 2.359 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1893 time to fit residues: 8.1846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 0.0870 chunk 178 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 225 optimal weight: 0.0670 chunk 67 optimal weight: 0.8980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN E 92 ASN F 195 GLN F 272 GLN F 422 ASN G 139 ASN G 195 GLN G 346 GLN G 412 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN N 35 ASN ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 20928 Z= 0.228 Angle : 0.557 8.995 28386 Z= 0.299 Chirality : 0.044 0.160 3261 Planarity : 0.004 0.056 3618 Dihedral : 4.871 23.531 2910 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.02 (0.16), residues: 2643 helix: 0.56 (0.25), residues: 420 sheet: -0.17 (0.16), residues: 954 loop : 0.09 (0.18), residues: 1269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 483 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 495 average time/residue: 0.3945 time to fit residues: 286.2275 Evaluate side-chains 496 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 480 time to evaluate : 2.302 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1919 time to fit residues: 8.9395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN C 210 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 332 HIS G 139 ASN G 195 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 20928 Z= 0.336 Angle : 0.592 8.964 28386 Z= 0.318 Chirality : 0.045 0.184 3261 Planarity : 0.004 0.042 3618 Dihedral : 4.935 20.990 2910 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2643 helix: 0.39 (0.24), residues: 420 sheet: -0.22 (0.16), residues: 954 loop : 0.01 (0.18), residues: 1269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 502 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 23 residues processed: 522 average time/residue: 0.3795 time to fit residues: 291.6493 Evaluate side-chains 511 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 488 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1839 time to fit residues: 11.1847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 0.0980 chunk 227 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN G 139 ASN G 195 GLN G 206 GLN G 307 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 20928 Z= 0.318 Angle : 0.584 8.349 28386 Z= 0.313 Chirality : 0.046 0.269 3261 Planarity : 0.004 0.041 3618 Dihedral : 4.872 20.242 2910 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.17 (0.16), residues: 2643 helix: 0.38 (0.25), residues: 423 sheet: -0.20 (0.16), residues: 945 loop : -0.05 (0.18), residues: 1275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 499 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 513 average time/residue: 0.3777 time to fit residues: 282.2051 Evaluate side-chains 514 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 497 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1928 time to fit residues: 9.2251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN G 139 ASN G 195 GLN ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 20928 Z= 0.289 Angle : 0.567 8.044 28386 Z= 0.304 Chirality : 0.045 0.188 3261 Planarity : 0.004 0.038 3618 Dihedral : 4.787 19.358 2910 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2643 helix: 0.45 (0.25), residues: 423 sheet: -0.18 (0.16), residues: 960 loop : -0.05 (0.18), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 496 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 502 average time/residue: 0.3808 time to fit residues: 281.4027 Evaluate side-chains 496 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 488 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2055 time to fit residues: 6.2373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN G 139 ASN G 195 GLN G 247 ASN ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 435 HIS ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN J 74 ASN ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 20928 Z= 0.290 Angle : 0.570 8.056 28386 Z= 0.304 Chirality : 0.045 0.217 3261 Planarity : 0.004 0.038 3618 Dihedral : 4.766 19.436 2910 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2643 helix: 0.49 (0.25), residues: 420 sheet: -0.20 (0.16), residues: 957 loop : -0.06 (0.18), residues: 1266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 499 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 509 average time/residue: 0.3993 time to fit residues: 301.0842 Evaluate side-chains 508 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 499 time to evaluate : 2.074 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2005 time to fit residues: 6.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 0.9990 chunk 241 optimal weight: 0.0770 chunk 219 optimal weight: 0.9980 chunk 234 optimal weight: 0.4980 chunk 240 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN C 195 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN G 139 ASN G 195 GLN G 247 ASN G 346 GLN G 353 ASN G 422 ASN G 435 HIS ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 20928 Z= 0.278 Angle : 0.565 8.089 28386 Z= 0.302 Chirality : 0.045 0.212 3261 Planarity : 0.004 0.037 3618 Dihedral : 4.730 19.122 2910 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.13 (0.17), residues: 2643 helix: 0.54 (0.25), residues: 417 sheet: -0.22 (0.17), residues: 930 loop : -0.03 (0.18), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 502 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 506 average time/residue: 0.3958 time to fit residues: 293.0988 Evaluate side-chains 501 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 493 time to evaluate : 2.407 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1969 time to fit residues: 6.3425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 247 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 260 optimal weight: 0.4980 chunk 239 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 159 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN G 195 GLN G 247 ASN G 353 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 20928 Z= 0.229 Angle : 0.547 8.219 28386 Z= 0.293 Chirality : 0.044 0.202 3261 Planarity : 0.004 0.036 3618 Dihedral : 4.641 18.748 2910 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2643 helix: 0.61 (0.25), residues: 420 sheet: -0.19 (0.17), residues: 930 loop : 0.01 (0.18), residues: 1293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 490 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 493 average time/residue: 0.3911 time to fit residues: 281.0754 Evaluate side-chains 493 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 490 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2003 time to fit residues: 4.1953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN C 195 GLN C 307 GLN F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN G 195 GLN G 247 ASN G 353 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN L 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105654 restraints weight = 28298.917| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.76 r_work: 0.3186 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 20928 Z= 0.471 Angle : 0.649 8.368 28386 Z= 0.347 Chirality : 0.049 0.273 3261 Planarity : 0.005 0.047 3618 Dihedral : 5.004 20.508 2910 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.33 (0.16), residues: 2643 helix: 0.17 (0.25), residues: 420 sheet: -0.20 (0.16), residues: 960 loop : -0.21 (0.18), residues: 1263 =============================================================================== Job complete usr+sys time: 5889.18 seconds wall clock time: 107 minutes 8.56 seconds (6428.56 seconds total)