Starting phenix.real_space_refine on Thu Mar 21 13:44:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/03_2024/7tjq_25929.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/03_2024/7tjq_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_25929/03_2024/7tjq_25929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/03_2024/7tjq_25929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/03_2024/7tjq_25929.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjq_25929/03_2024/7tjq_25929.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.13, per 1000 atoms: 0.54 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: 8.67 Conformation dependent library (CDL) restraints added in 3.9 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: 3.02 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: 8.97 Time building geometry restraints manager: 9.32 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: 11873 17.97 - 35.93: 664 35.93 - 53.90: 144 53.90 - 71.87: 63 71.87 - 89.83: 18 Dihedral angle restraints: 12762 sinusoidal: 5082 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 12759 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 18.240 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 59.020 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.220 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.790 ------------------------------------------------------------------------------- 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 : 13.284 89.834 7716 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 % Allowed : 4.82 % Favored : 94.15 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 50 HIS 0.007 0.002 HIS G 332 PHE 0.021 0.002 PHE I 29 TYR 0.037 0.005 TYR E 49 ARG 0.025 0.003 ARG C 163 *********************** 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 : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7718 (pmt170) REVERT: B 26 SER cc_start: 0.7874 (p) cc_final: 0.7521 (p) REVERT: B 96 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7713 (mpt180) REVERT: C 79 ARG cc_start: 0.6960 (mtm-85) cc_final: 0.6640 (mtm-85) REVERT: C 81 LEU cc_start: 0.8293 (tp) cc_final: 0.8081 (tp) REVERT: C 133 GLU cc_start: 0.6426 (tp30) cc_final: 0.6203 (tp30) REVERT: C 197 ASN cc_start: 0.8071 (p0) cc_final: 0.7747 (p0) REVERT: C 343 VAL cc_start: 0.8589 (p) cc_final: 0.8247 (m) REVERT: C 399 ILE cc_start: 0.7975 (mm) cc_final: 0.7774 (mt) REVERT: E 74 THR cc_start: 0.7780 (m) cc_final: 0.7345 (p) REVERT: F 62 ASP cc_start: 0.7274 (m-30) cc_final: 0.6901 (m-30) REVERT: F 133 GLU cc_start: 0.6759 (tp30) cc_final: 0.6224 (tp30) REVERT: F 163 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.7160 (mtm-85) REVERT: F 174 THR cc_start: 0.8077 (m) cc_final: 0.7806 (m) REVERT: F 189 MET cc_start: 0.6993 (mmt) cc_final: 0.6465 (mmt) REVERT: F 192 SER cc_start: 0.7605 (m) cc_final: 0.7253 (p) REVERT: F 205 ARG cc_start: 0.6661 (ttp80) cc_final: 0.6311 (ttp80) REVERT: F 223 THR cc_start: 0.8175 (m) cc_final: 0.7843 (p) REVERT: F 256 PHE cc_start: 0.8144 (p90) cc_final: 0.7840 (p90) REVERT: F 343 VAL cc_start: 0.8360 (p) cc_final: 0.8041 (m) REVERT: F 401 LYS cc_start: 0.7600 (tttp) cc_final: 0.7318 (mtpp) REVERT: F 450 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7556 (mmtt) REVERT: F 454 ASP cc_start: 0.6662 (m-30) cc_final: 0.6446 (m-30) REVERT: F 464 PHE cc_start: 0.7962 (m-80) cc_final: 0.7758 (m-80) REVERT: G 20 LYS cc_start: 0.7674 (tttt) cc_final: 0.7443 (tttm) REVERT: G 170 SER cc_start: 0.7712 (p) cc_final: 0.7472 (m) REVERT: G 177 ILE cc_start: 0.7837 (mt) cc_final: 0.7634 (mt) REVERT: G 192 SER cc_start: 0.7664 (m) cc_final: 0.7284 (p) REVERT: G 198 ARG cc_start: 0.7139 (ttm-80) cc_final: 0.6759 (ttm-80) REVERT: G 205 ARG cc_start: 0.6429 (ttp80) cc_final: 0.6177 (ttp80) REVERT: G 219 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7315 (mmmm) REVERT: G 305 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6040 (mt-10) REVERT: G 318 VAL cc_start: 0.8358 (p) cc_final: 0.8113 (t) REVERT: G 343 VAL cc_start: 0.8326 (p) cc_final: 0.7895 (m) REVERT: G 454 ASP cc_start: 0.6747 (m-30) cc_final: 0.6470 (m-30) REVERT: I 52 SER cc_start: 0.8229 (p) cc_final: 0.8013 (t) REVERT: K 50 ILE cc_start: 0.8106 (mm) cc_final: 0.7819 (mm) REVERT: M 27 SER cc_start: 0.7611 (p) cc_final: 0.7375 (p) REVERT: N 52 SER cc_start: 0.8350 (p) cc_final: 0.8098 (t) REVERT: O 27 SER cc_start: 0.8330 (p) cc_final: 0.7976 (p) outliers start: 23 outliers final: 7 residues processed: 621 average time/residue: 0.3639 time to fit residues: 330.7890 Evaluate side-chains 542 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 533 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain I residue 12 VAL 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: 1.9990 chunk 105 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 124 optimal weight: 0.0870 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- 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: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20928 Z= 0.421 Angle : 0.696 9.277 28386 Z= 0.380 Chirality : 0.049 0.238 3261 Planarity : 0.005 0.048 3618 Dihedral : 6.987 59.728 3180 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.45 % Allowed : 11.20 % Favored : 86.35 % 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: -0.29 (0.16), residues: 2643 helix: 0.14 (0.24), residues: 420 sheet: -0.15 (0.17), residues: 903 loop : -0.18 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 50 HIS 0.008 0.002 HIS G 368 PHE 0.027 0.003 PHE J 29 TYR 0.033 0.003 TYR K 51 ARG 0.007 0.001 ARG G 253 *********************** 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 595 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 540 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.7732 (t) cc_final: 0.7359 (t) REVERT: C 70 GLU cc_start: 0.6504 (tp30) cc_final: 0.6256 (tp30) REVERT: C 71 LEU cc_start: 0.7839 (tp) cc_final: 0.7610 (tp) REVERT: C 75 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8160 (mtmt) REVERT: C 81 LEU cc_start: 0.8181 (tp) cc_final: 0.7940 (tp) REVERT: C 133 GLU cc_start: 0.6673 (tp30) cc_final: 0.6384 (tp30) REVERT: C 197 ASN cc_start: 0.8177 (p0) cc_final: 0.7196 (p0) REVERT: C 223 THR cc_start: 0.8448 (m) cc_final: 0.8242 (m) REVERT: C 226 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6934 (mt-10) REVERT: C 248 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7221 (mtp85) REVERT: C 318 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8206 (t) REVERT: C 343 VAL cc_start: 0.8542 (p) cc_final: 0.8229 (m) REVERT: C 399 ILE cc_start: 0.8018 (mm) cc_final: 0.7752 (mt) REVERT: C 412 ASN cc_start: 0.7450 (p0) cc_final: 0.7222 (p0) REVERT: C 454 ASP cc_start: 0.6887 (m-30) cc_final: 0.6682 (m-30) REVERT: E 74 THR cc_start: 0.8063 (m) cc_final: 0.7529 (p) REVERT: F 62 ASP cc_start: 0.7235 (m-30) cc_final: 0.6930 (m-30) REVERT: F 133 GLU cc_start: 0.6754 (tp30) cc_final: 0.6286 (tp30) REVERT: F 189 MET cc_start: 0.6930 (mmt) cc_final: 0.6476 (mmt) REVERT: F 192 SER cc_start: 0.7589 (m) cc_final: 0.7152 (p) REVERT: F 206 GLN cc_start: 0.7331 (mt0) cc_final: 0.7067 (mt0) REVERT: F 245 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7854 (mm) REVERT: F 250 MET cc_start: 0.6225 (mmm) cc_final: 0.6016 (mmm) REVERT: F 343 VAL cc_start: 0.8452 (p) cc_final: 0.8126 (m) REVERT: F 454 ASP cc_start: 0.6682 (m-30) cc_final: 0.6435 (m-30) REVERT: F 464 PHE cc_start: 0.8007 (m-80) cc_final: 0.7801 (m-80) REVERT: G 20 LYS cc_start: 0.7912 (tttt) cc_final: 0.7702 (tttm) REVERT: G 40 ARG cc_start: 0.7722 (tmm160) cc_final: 0.7322 (tmm160) REVERT: G 73 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8251 (mp) REVERT: G 163 ARG cc_start: 0.7309 (ttm-80) cc_final: 0.7018 (mtm-85) REVERT: G 177 ILE cc_start: 0.7846 (mt) cc_final: 0.7560 (mt) REVERT: G 192 SER cc_start: 0.7442 (m) cc_final: 0.7188 (p) REVERT: G 197 ASN cc_start: 0.8266 (p0) cc_final: 0.7543 (p0) REVERT: G 198 ARG cc_start: 0.7032 (ttm-80) cc_final: 0.6630 (ttm-80) REVERT: G 219 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7351 (mmmm) REVERT: G 223 THR cc_start: 0.8347 (m) cc_final: 0.7900 (p) REVERT: G 280 ASP cc_start: 0.7028 (t70) cc_final: 0.6730 (t70) REVERT: G 318 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8051 (t) REVERT: G 343 VAL cc_start: 0.8391 (p) cc_final: 0.8017 (m) REVERT: G 353 ASN cc_start: 0.7214 (p0) cc_final: 0.6934 (p0) REVERT: G 454 ASP cc_start: 0.6738 (m-30) cc_final: 0.6483 (m-30) REVERT: I 7 SER cc_start: 0.7964 (p) cc_final: 0.7680 (t) REVERT: J 7 SER cc_start: 0.7755 (p) cc_final: 0.7516 (t) REVERT: K 50 ILE cc_start: 0.8216 (mm) cc_final: 0.7908 (mm) REVERT: L 79 GLN cc_start: 0.7427 (mm110) cc_final: 0.7118 (mm-40) REVERT: M 27 SER cc_start: 0.7773 (p) cc_final: 0.7463 (p) REVERT: N 52 SER cc_start: 0.8389 (p) cc_final: 0.7988 (t) REVERT: O 27 SER cc_start: 0.8160 (p) cc_final: 0.7868 (p) outliers start: 55 outliers final: 34 residues processed: 563 average time/residue: 0.3677 time to fit residues: 302.7716 Evaluate side-chains 551 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 513 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain O residue 9 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 307 GLN G 139 ASN G 202 ASN G 247 ASN G 346 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN N 35 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2041 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= 0.458 Angle : 0.673 9.678 28386 Z= 0.365 Chirality : 0.048 0.200 3261 Planarity : 0.005 0.054 3618 Dihedral : 6.617 59.701 3167 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.99 % Allowed : 13.57 % Favored : 83.44 % 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: -0.44 (0.16), residues: 2643 helix: -0.03 (0.24), residues: 420 sheet: -0.28 (0.17), residues: 933 loop : -0.24 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP O 37 HIS 0.009 0.002 HIS C 332 PHE 0.025 0.003 PHE J 29 TYR 0.033 0.003 TYR K 51 ARG 0.008 0.001 ARG F 129 *********************** 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 597 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 530 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8200 (m-80) cc_final: 0.7971 (m-80) REVERT: B 26 SER cc_start: 0.7892 (p) cc_final: 0.7562 (p) REVERT: B 102 THR cc_start: 0.8011 (t) cc_final: 0.7614 (t) REVERT: C 71 LEU cc_start: 0.7803 (tp) cc_final: 0.7553 (tp) REVERT: C 81 LEU cc_start: 0.8193 (tp) cc_final: 0.7984 (tp) REVERT: C 189 MET cc_start: 0.6753 (tpp) cc_final: 0.6493 (mpp) REVERT: C 195 GLN cc_start: 0.7627 (mt0) cc_final: 0.7314 (mt0) REVERT: C 223 THR cc_start: 0.8399 (m) cc_final: 0.8051 (p) REVERT: C 226 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6969 (mt-10) REVERT: C 248 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7255 (mtp85) REVERT: C 318 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8228 (t) REVERT: C 343 VAL cc_start: 0.8469 (p) cc_final: 0.8202 (m) REVERT: C 399 ILE cc_start: 0.7966 (mm) cc_final: 0.7732 (mt) REVERT: C 412 ASN cc_start: 0.7428 (p0) cc_final: 0.7227 (p0) REVERT: C 454 ASP cc_start: 0.6900 (m-30) cc_final: 0.6687 (m-30) REVERT: E 74 THR cc_start: 0.8004 (m) cc_final: 0.7520 (p) REVERT: F 62 ASP cc_start: 0.7179 (m-30) cc_final: 0.6890 (m-30) REVERT: F 133 GLU cc_start: 0.6820 (tp30) cc_final: 0.6339 (tp30) REVERT: F 189 MET cc_start: 0.6875 (mmt) cc_final: 0.6465 (mmt) REVERT: F 245 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7859 (mm) REVERT: F 250 MET cc_start: 0.6273 (mmm) cc_final: 0.5935 (tmm) REVERT: F 343 VAL cc_start: 0.8446 (p) cc_final: 0.8093 (m) REVERT: F 378 LEU cc_start: 0.8279 (mt) cc_final: 0.7516 (mp) REVERT: F 401 LYS cc_start: 0.7832 (ttpp) cc_final: 0.7628 (ttpp) REVERT: F 412 ASN cc_start: 0.7743 (p0) cc_final: 0.7360 (p0) REVERT: F 454 ASP cc_start: 0.6732 (m-30) cc_final: 0.6484 (m-30) REVERT: G 20 LYS cc_start: 0.7901 (tttt) cc_final: 0.7700 (tttm) REVERT: G 70 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: G 75 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7962 (mtmt) REVERT: G 129 ARG cc_start: 0.7383 (ttp-170) cc_final: 0.7149 (ttp-170) REVERT: G 131 GLU cc_start: 0.7090 (tt0) cc_final: 0.6650 (tt0) REVERT: G 156 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6625 (ptt-90) REVERT: G 163 ARG cc_start: 0.7236 (ttm-80) cc_final: 0.7036 (mtm-85) REVERT: G 177 ILE cc_start: 0.7822 (mt) cc_final: 0.7541 (mt) REVERT: G 178 ASN cc_start: 0.7555 (t0) cc_final: 0.7337 (t0) REVERT: G 197 ASN cc_start: 0.8301 (p0) cc_final: 0.7640 (p0) REVERT: G 223 THR cc_start: 0.8353 (m) cc_final: 0.7881 (p) REVERT: G 280 ASP cc_start: 0.7137 (t70) cc_final: 0.6792 (t70) REVERT: G 318 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8111 (t) REVERT: G 329 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7137 (ttm-80) REVERT: G 343 VAL cc_start: 0.8386 (p) cc_final: 0.8077 (m) REVERT: G 353 ASN cc_start: 0.7233 (p0) cc_final: 0.6989 (p0) REVERT: G 454 ASP cc_start: 0.6750 (m-30) cc_final: 0.6452 (m-30) REVERT: G 464 PHE cc_start: 0.8011 (m-80) cc_final: 0.7755 (m-80) REVERT: I 7 SER cc_start: 0.7963 (p) cc_final: 0.7660 (t) REVERT: J 7 SER cc_start: 0.7760 (p) cc_final: 0.7501 (t) REVERT: K 50 ILE cc_start: 0.8256 (mm) cc_final: 0.7948 (mm) REVERT: L 79 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7136 (mm-40) REVERT: N 52 SER cc_start: 0.8338 (p) cc_final: 0.7999 (t) REVERT: O 27 SER cc_start: 0.8146 (p) cc_final: 0.7898 (p) outliers start: 67 outliers final: 46 residues processed: 561 average time/residue: 0.3593 time to fit residues: 298.2141 Evaluate side-chains 564 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 513 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain O residue 9 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 0.0980 chunk 178 optimal weight: 0.8980 chunk 123 optimal weight: 0.0670 chunk 26 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 225 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN F 195 GLN F 332 HIS G 46 ASN G 139 ASN G 247 ASN G 346 GLN G 412 ASN G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN M 55 ASN N 35 ASN O 28 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20928 Z= 0.174 Angle : 0.541 8.963 28386 Z= 0.290 Chirality : 0.043 0.164 3261 Planarity : 0.004 0.042 3618 Dihedral : 6.129 59.217 3167 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.63 % Allowed : 14.73 % Favored : 82.64 % 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: -0.05 (0.16), residues: 2643 helix: 0.57 (0.25), residues: 420 sheet: -0.14 (0.16), residues: 948 loop : 0.02 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 50 HIS 0.006 0.001 HIS C 332 PHE 0.012 0.002 PHE F 334 TYR 0.013 0.001 TYR K 51 ARG 0.006 0.000 ARG C 329 *********************** 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 552 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 493 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 TYR cc_start: 0.8149 (m-80) cc_final: 0.7948 (m-80) REVERT: B 102 THR cc_start: 0.8105 (t) cc_final: 0.7740 (t) REVERT: C 70 GLU cc_start: 0.6419 (tp30) cc_final: 0.6152 (tp30) REVERT: C 133 GLU cc_start: 0.6749 (tp30) cc_final: 0.6449 (tp30) REVERT: C 163 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.6852 (ttm170) REVERT: C 192 SER cc_start: 0.7934 (t) cc_final: 0.7564 (p) REVERT: C 195 GLN cc_start: 0.7543 (mt0) cc_final: 0.7174 (mt0) REVERT: C 223 THR cc_start: 0.8397 (m) cc_final: 0.8036 (p) REVERT: C 253 ARG cc_start: 0.7083 (ttp-110) cc_final: 0.6757 (ttp80) REVERT: C 318 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8198 (t) REVERT: C 343 VAL cc_start: 0.8525 (p) cc_final: 0.8258 (m) REVERT: C 399 ILE cc_start: 0.7939 (mm) cc_final: 0.7723 (mt) REVERT: D 71 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7504 (pmt-80) REVERT: E 74 THR cc_start: 0.7991 (m) cc_final: 0.7502 (p) REVERT: F 62 ASP cc_start: 0.7157 (m-30) cc_final: 0.6866 (m-30) REVERT: F 133 GLU cc_start: 0.6796 (tp30) cc_final: 0.6382 (tp30) REVERT: F 163 ARG cc_start: 0.7389 (ttm-80) cc_final: 0.7002 (mtm-85) REVERT: F 189 MET cc_start: 0.6755 (mmt) cc_final: 0.6453 (mmt) REVERT: F 250 MET cc_start: 0.6206 (mmm) cc_final: 0.5950 (tmm) REVERT: F 343 VAL cc_start: 0.8491 (p) cc_final: 0.8124 (m) REVERT: F 397 VAL cc_start: 0.7765 (t) cc_final: 0.7416 (m) REVERT: F 411 THR cc_start: 0.8188 (p) cc_final: 0.7947 (p) REVERT: F 454 ASP cc_start: 0.6699 (m-30) cc_final: 0.6460 (m-30) REVERT: G 70 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: G 79 ARG cc_start: 0.7280 (mtm-85) cc_final: 0.6986 (mtm-85) REVERT: G 129 ARG cc_start: 0.7402 (ttp-170) cc_final: 0.6987 (ptm-80) REVERT: G 131 GLU cc_start: 0.7020 (tt0) cc_final: 0.6619 (tt0) REVERT: G 144 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7655 (t) REVERT: G 156 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6601 (ptt-90) REVERT: G 167 ASP cc_start: 0.6739 (m-30) cc_final: 0.6477 (m-30) REVERT: G 178 ASN cc_start: 0.7536 (t0) cc_final: 0.7325 (t0) REVERT: G 223 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7926 (p) REVERT: G 280 ASP cc_start: 0.7062 (t70) cc_final: 0.6740 (t70) REVERT: G 329 ARG cc_start: 0.7401 (ttm110) cc_final: 0.7150 (mtp85) REVERT: G 343 VAL cc_start: 0.8455 (p) cc_final: 0.8144 (m) REVERT: G 353 ASN cc_start: 0.7183 (p0) cc_final: 0.6929 (p0) REVERT: G 454 ASP cc_start: 0.6709 (m-30) cc_final: 0.6461 (m-30) REVERT: G 464 PHE cc_start: 0.8004 (m-80) cc_final: 0.7725 (m-80) REVERT: I 7 SER cc_start: 0.7946 (p) cc_final: 0.7636 (t) REVERT: J 7 SER cc_start: 0.7701 (p) cc_final: 0.7443 (t) REVERT: K 50 ILE cc_start: 0.8090 (mm) cc_final: 0.7781 (mm) REVERT: L 79 GLN cc_start: 0.7442 (mm110) cc_final: 0.7124 (mm-40) REVERT: N 52 SER cc_start: 0.8226 (p) cc_final: 0.8016 (t) REVERT: O 25 SER cc_start: 0.8015 (p) cc_final: 0.7781 (p) outliers start: 59 outliers final: 32 residues processed: 526 average time/residue: 0.3748 time to fit residues: 285.7031 Evaluate side-chains 535 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 497 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN C 422 ASN F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 422 ASN G 46 ASN G 233 ASN G 247 ASN ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 GLN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 20928 Z= 0.610 Angle : 0.717 9.439 28386 Z= 0.386 Chirality : 0.052 0.194 3261 Planarity : 0.005 0.058 3618 Dihedral : 6.572 59.870 3166 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.66 % Allowed : 15.17 % Favored : 81.17 % 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: -0.58 (0.16), residues: 2643 helix: -0.17 (0.24), residues: 420 sheet: -0.30 (0.17), residues: 924 loop : -0.38 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP O 37 HIS 0.009 0.002 HIS C 332 PHE 0.030 0.003 PHE J 29 TYR 0.040 0.003 TYR K 51 ARG 0.009 0.001 ARG F 129 *********************** 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 604 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 522 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.6850 (pmt-80) REVERT: B 26 SER cc_start: 0.7904 (p) cc_final: 0.7597 (p) REVERT: B 102 THR cc_start: 0.8188 (t) cc_final: 0.7806 (t) REVERT: C 110 CYS cc_start: 0.5398 (OUTLIER) cc_final: 0.5147 (m) REVERT: C 192 SER cc_start: 0.8172 (t) cc_final: 0.7814 (p) REVERT: C 195 GLN cc_start: 0.7617 (mt0) cc_final: 0.7330 (mt0) REVERT: C 253 ARG cc_start: 0.7108 (ttp-110) cc_final: 0.6888 (ttp80) REVERT: C 318 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8195 (t) REVERT: C 343 VAL cc_start: 0.8395 (p) cc_final: 0.8145 (m) REVERT: C 399 ILE cc_start: 0.8018 (mm) cc_final: 0.7791 (mt) REVERT: D 71 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7364 (pmt-80) REVERT: E 74 THR cc_start: 0.8021 (m) cc_final: 0.7536 (p) REVERT: F 62 ASP cc_start: 0.7162 (m-30) cc_final: 0.6906 (m-30) REVERT: F 133 GLU cc_start: 0.6862 (tp30) cc_final: 0.6328 (tp30) REVERT: F 163 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7129 (mtm-85) REVERT: F 189 MET cc_start: 0.6789 (mmt) cc_final: 0.6343 (mmt) REVERT: F 343 VAL cc_start: 0.8399 (p) cc_final: 0.8088 (m) REVERT: F 401 LYS cc_start: 0.7845 (ttpp) cc_final: 0.7592 (ptmm) REVERT: F 411 THR cc_start: 0.8301 (p) cc_final: 0.8088 (p) REVERT: G 70 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: G 129 ARG cc_start: 0.7416 (ttp-170) cc_final: 0.6981 (ttp-170) REVERT: G 131 GLU cc_start: 0.7084 (tt0) cc_final: 0.6669 (tt0) REVERT: G 156 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6668 (ptt-90) REVERT: G 167 ASP cc_start: 0.6788 (m-30) cc_final: 0.6528 (m-30) REVERT: G 178 ASN cc_start: 0.7585 (t0) cc_final: 0.7293 (t0) REVERT: G 197 ASN cc_start: 0.8260 (p0) cc_final: 0.7641 (p0) REVERT: G 223 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7901 (p) REVERT: G 280 ASP cc_start: 0.7196 (t70) cc_final: 0.6871 (t70) REVERT: G 343 VAL cc_start: 0.8380 (p) cc_final: 0.8089 (m) REVERT: G 353 ASN cc_start: 0.7207 (p0) cc_final: 0.6913 (p0) REVERT: G 454 ASP cc_start: 0.6835 (m-30) cc_final: 0.6549 (m-30) REVERT: G 464 PHE cc_start: 0.7988 (m-80) cc_final: 0.7736 (m-80) REVERT: I 7 SER cc_start: 0.7968 (p) cc_final: 0.7660 (t) REVERT: J 7 SER cc_start: 0.7732 (p) cc_final: 0.7453 (t) REVERT: K 50 ILE cc_start: 0.8310 (mm) cc_final: 0.8011 (mm) REVERT: M 98 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7946 (m) REVERT: N 52 SER cc_start: 0.8282 (p) cc_final: 0.8013 (t) outliers start: 82 outliers final: 58 residues processed: 565 average time/residue: 0.3652 time to fit residues: 302.1488 Evaluate side-chains 567 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 501 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 358 ASN Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain G residue 457 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain O residue 9 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 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 46 ASN G 346 GLN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20928 Z= 0.291 Angle : 0.583 8.312 28386 Z= 0.314 Chirality : 0.045 0.231 3261 Planarity : 0.004 0.050 3618 Dihedral : 6.244 59.175 3166 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.99 % Allowed : 16.29 % Favored : 80.72 % 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: -0.35 (0.16), residues: 2643 helix: 0.20 (0.25), residues: 420 sheet: -0.25 (0.17), residues: 924 loop : -0.21 (0.18), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 50 HIS 0.007 0.001 HIS C 332 PHE 0.016 0.002 PHE J 29 TYR 0.021 0.002 TYR K 51 ARG 0.006 0.000 ARG G 252 *********************** 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 562 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 495 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.8232 (t) cc_final: 0.7884 (t) REVERT: C 110 CYS cc_start: 0.5252 (OUTLIER) cc_final: 0.5003 (m) REVERT: C 133 GLU cc_start: 0.6657 (tp30) cc_final: 0.6438 (tp30) REVERT: C 192 SER cc_start: 0.8021 (t) cc_final: 0.7694 (p) REVERT: C 195 GLN cc_start: 0.7561 (mt0) cc_final: 0.7274 (mt0) REVERT: C 318 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8217 (t) REVERT: C 343 VAL cc_start: 0.8413 (p) cc_final: 0.8159 (m) REVERT: C 399 ILE cc_start: 0.7979 (mm) cc_final: 0.7740 (mt) REVERT: D 71 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7412 (pmt-80) REVERT: E 74 THR cc_start: 0.8019 (m) cc_final: 0.7572 (p) REVERT: F 62 ASP cc_start: 0.7084 (m-30) cc_final: 0.6823 (m-30) REVERT: F 133 GLU cc_start: 0.6785 (tp30) cc_final: 0.6362 (tp30) REVERT: F 163 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.7084 (mtm-85) REVERT: F 189 MET cc_start: 0.6761 (mmt) cc_final: 0.6345 (mmt) REVERT: F 343 VAL cc_start: 0.8430 (p) cc_final: 0.8081 (m) REVERT: F 401 LYS cc_start: 0.7885 (ttpp) cc_final: 0.7650 (ptmm) REVERT: G 70 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: G 75 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7950 (mttt) REVERT: G 131 GLU cc_start: 0.7026 (tt0) cc_final: 0.6614 (tt0) REVERT: G 156 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6582 (ptt-90) REVERT: G 167 ASP cc_start: 0.6753 (m-30) cc_final: 0.6452 (m-30) REVERT: G 197 ASN cc_start: 0.8279 (p0) cc_final: 0.7723 (p0) REVERT: G 280 ASP cc_start: 0.7116 (t70) cc_final: 0.6796 (t70) REVERT: G 343 VAL cc_start: 0.8421 (p) cc_final: 0.8127 (m) REVERT: G 353 ASN cc_start: 0.7154 (p0) cc_final: 0.6889 (p0) REVERT: G 454 ASP cc_start: 0.6767 (m-30) cc_final: 0.6513 (m-30) REVERT: G 464 PHE cc_start: 0.7986 (m-80) cc_final: 0.7713 (m-80) REVERT: I 7 SER cc_start: 0.7939 (p) cc_final: 0.7627 (t) REVERT: K 50 ILE cc_start: 0.8183 (mm) cc_final: 0.7895 (mm) outliers start: 67 outliers final: 49 residues processed: 529 average time/residue: 0.3667 time to fit residues: 284.7557 Evaluate side-chains 548 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 494 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 390 CYS Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain O residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 0.0060 chunk 28 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 46 ASN G 139 ASN G 247 ASN G 346 GLN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2696 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= 0.276 Angle : 0.561 8.351 28386 Z= 0.301 Chirality : 0.045 0.174 3261 Planarity : 0.004 0.043 3618 Dihedral : 6.086 59.785 3166 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.03 % Allowed : 16.87 % Favored : 80.10 % 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: -0.24 (0.16), residues: 2643 helix: 0.38 (0.25), residues: 423 sheet: -0.19 (0.17), residues: 924 loop : -0.17 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 50 HIS 0.006 0.001 HIS C 332 PHE 0.017 0.002 PHE J 29 TYR 0.020 0.002 TYR K 51 ARG 0.006 0.000 ARG G 252 *********************** 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 568 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 500 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6809 (pmt-80) REVERT: B 26 SER cc_start: 0.7809 (p) cc_final: 0.7486 (p) REVERT: C 129 ARG cc_start: 0.7235 (mtp-110) cc_final: 0.6946 (ptm-80) REVERT: C 133 GLU cc_start: 0.6688 (tp30) cc_final: 0.6408 (tp30) REVERT: C 192 SER cc_start: 0.7986 (t) cc_final: 0.7634 (p) REVERT: C 195 GLN cc_start: 0.7560 (mt0) cc_final: 0.7228 (mt0) REVERT: C 305 GLU cc_start: 0.6481 (tp30) cc_final: 0.6157 (mp0) REVERT: C 318 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8240 (t) REVERT: C 343 VAL cc_start: 0.8421 (p) cc_final: 0.8178 (m) REVERT: C 399 ILE cc_start: 0.7971 (mm) cc_final: 0.7723 (mt) REVERT: D 71 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7398 (pmt-80) REVERT: E 74 THR cc_start: 0.8008 (m) cc_final: 0.7588 (p) REVERT: F 62 ASP cc_start: 0.7092 (m-30) cc_final: 0.6817 (m-30) REVERT: F 133 GLU cc_start: 0.6791 (tp30) cc_final: 0.6351 (tp30) REVERT: F 163 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.6926 (mtm-85) REVERT: F 189 MET cc_start: 0.6751 (mmt) cc_final: 0.6337 (mmt) REVERT: F 343 VAL cc_start: 0.8419 (p) cc_final: 0.8088 (m) REVERT: F 401 LYS cc_start: 0.7860 (ttpp) cc_final: 0.7651 (ptmm) REVERT: G 70 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: G 131 GLU cc_start: 0.7015 (tt0) cc_final: 0.6614 (tt0) REVERT: G 144 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7668 (t) REVERT: G 156 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6616 (ptt-90) REVERT: G 167 ASP cc_start: 0.6753 (m-30) cc_final: 0.6407 (m-30) REVERT: G 280 ASP cc_start: 0.7117 (t70) cc_final: 0.6816 (t70) REVERT: G 343 VAL cc_start: 0.8409 (p) cc_final: 0.8142 (m) REVERT: G 353 ASN cc_start: 0.7172 (p0) cc_final: 0.6893 (p0) REVERT: G 454 ASP cc_start: 0.6796 (m-30) cc_final: 0.6518 (m-30) REVERT: H 78 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7094 (mt) REVERT: K 50 ILE cc_start: 0.8179 (mm) cc_final: 0.7865 (mm) REVERT: M 98 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7983 (m) outliers start: 68 outliers final: 50 residues processed: 538 average time/residue: 0.3678 time to fit residues: 288.4829 Evaluate side-chains 556 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 498 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 69 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 197 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** 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 G 139 ASN G 195 GLN G 346 GLN ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 435 HIS ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN L 79 GLN ** O 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2781 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= 0.274 Angle : 0.555 8.336 28386 Z= 0.298 Chirality : 0.044 0.168 3261 Planarity : 0.004 0.042 3618 Dihedral : 5.986 58.113 3166 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.44 % Allowed : 16.87 % Favored : 79.70 % 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: -0.20 (0.16), residues: 2643 helix: 0.43 (0.25), residues: 423 sheet: -0.14 (0.17), residues: 930 loop : -0.17 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 50 HIS 0.005 0.001 HIS C 332 PHE 0.018 0.002 PHE J 29 TYR 0.020 0.002 TYR K 51 ARG 0.005 0.000 ARG G 252 *********************** 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 574 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 497 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6698 (pmt-80) REVERT: C 110 CYS cc_start: 0.5198 (OUTLIER) cc_final: 0.4977 (m) REVERT: C 126 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7142 (mttm) REVERT: C 192 SER cc_start: 0.7979 (t) cc_final: 0.7618 (p) REVERT: C 195 GLN cc_start: 0.7554 (mt0) cc_final: 0.7221 (mt0) REVERT: C 318 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8243 (t) REVERT: C 343 VAL cc_start: 0.8409 (p) cc_final: 0.8178 (m) REVERT: C 399 ILE cc_start: 0.7964 (mm) cc_final: 0.7709 (mt) REVERT: D 71 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7362 (pmt-80) REVERT: E 74 THR cc_start: 0.8002 (m) cc_final: 0.7595 (p) REVERT: F 62 ASP cc_start: 0.7081 (m-30) cc_final: 0.6803 (m-30) REVERT: F 133 GLU cc_start: 0.6792 (tp30) cc_final: 0.6347 (tp30) REVERT: F 163 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.7145 (mtm-85) REVERT: F 189 MET cc_start: 0.6734 (mmt) cc_final: 0.6313 (mmt) REVERT: F 343 VAL cc_start: 0.8424 (p) cc_final: 0.8087 (m) REVERT: G 70 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: G 131 GLU cc_start: 0.6944 (tt0) cc_final: 0.6567 (tt0) REVERT: G 156 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6625 (ptt-90) REVERT: G 167 ASP cc_start: 0.6753 (m-30) cc_final: 0.6376 (m-30) REVERT: G 197 ASN cc_start: 0.8274 (p0) cc_final: 0.7708 (p0) REVERT: G 280 ASP cc_start: 0.7124 (t70) cc_final: 0.6832 (t70) REVERT: G 343 VAL cc_start: 0.8404 (p) cc_final: 0.8129 (m) REVERT: G 353 ASN cc_start: 0.7144 (p0) cc_final: 0.6876 (p0) REVERT: G 454 ASP cc_start: 0.6852 (m-30) cc_final: 0.6572 (m-30) REVERT: K 50 ILE cc_start: 0.8179 (mm) cc_final: 0.7858 (mm) REVERT: M 98 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7972 (m) outliers start: 77 outliers final: 56 residues processed: 538 average time/residue: 0.3882 time to fit residues: 306.7170 Evaluate side-chains 561 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 498 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 431 GLU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 0.6980 chunk 241 optimal weight: 0.0370 chunk 219 optimal weight: 0.8980 chunk 234 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 102 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN G 139 ASN G 195 GLN G 247 ASN G 346 GLN G 351 ASN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN L 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20928 Z= 0.213 Angle : 0.535 8.172 28386 Z= 0.286 Chirality : 0.044 0.269 3261 Planarity : 0.004 0.037 3618 Dihedral : 5.875 59.845 3166 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.77 % Allowed : 17.72 % Favored : 79.52 % 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: -0.12 (0.16), residues: 2643 helix: 0.58 (0.25), residues: 423 sheet: -0.16 (0.17), residues: 897 loop : -0.09 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 50 HIS 0.005 0.001 HIS C 332 PHE 0.013 0.001 PHE J 29 TYR 0.019 0.002 TYR A 53 ARG 0.007 0.000 ARG F 129 *********************** 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 566 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 504 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.7991 (p) REVERT: C 110 CYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4913 (m) REVERT: C 192 SER cc_start: 0.7922 (t) cc_final: 0.7570 (p) REVERT: C 195 GLN cc_start: 0.7524 (mt0) cc_final: 0.7189 (mt0) REVERT: C 305 GLU cc_start: 0.6456 (tp30) cc_final: 0.6139 (mp0) REVERT: C 318 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8201 (t) REVERT: C 343 VAL cc_start: 0.8436 (p) cc_final: 0.8200 (m) REVERT: C 399 ILE cc_start: 0.7949 (mm) cc_final: 0.7689 (mt) REVERT: D 71 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7384 (pmt-80) REVERT: E 74 THR cc_start: 0.7994 (m) cc_final: 0.7604 (p) REVERT: F 21 GLU cc_start: 0.6295 (tp30) cc_final: 0.6042 (tp30) REVERT: F 62 ASP cc_start: 0.7102 (m-30) cc_final: 0.6798 (m-30) REVERT: F 133 GLU cc_start: 0.6780 (tp30) cc_final: 0.6346 (tp30) REVERT: F 163 ARG cc_start: 0.7402 (ttm-80) cc_final: 0.7088 (mtm-85) REVERT: F 189 MET cc_start: 0.6712 (mmt) cc_final: 0.6305 (mmt) REVERT: F 250 MET cc_start: 0.6149 (mmm) cc_final: 0.5897 (tmm) REVERT: F 343 VAL cc_start: 0.8416 (p) cc_final: 0.8079 (m) REVERT: F 397 VAL cc_start: 0.7685 (t) cc_final: 0.7374 (m) REVERT: G 70 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6209 (mp0) REVERT: G 131 GLU cc_start: 0.6912 (tt0) cc_final: 0.6560 (tt0) REVERT: G 144 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7680 (t) REVERT: G 156 ARG cc_start: 0.6996 (ptm-80) cc_final: 0.6616 (ptt-90) REVERT: G 167 ASP cc_start: 0.6708 (m-30) cc_final: 0.6277 (m-30) REVERT: G 197 ASN cc_start: 0.8260 (p0) cc_final: 0.7722 (p0) REVERT: G 280 ASP cc_start: 0.7103 (t70) cc_final: 0.6818 (t70) REVERT: G 329 ARG cc_start: 0.7438 (ttm110) cc_final: 0.7107 (ttm-80) REVERT: G 343 VAL cc_start: 0.8419 (p) cc_final: 0.8161 (m) REVERT: G 353 ASN cc_start: 0.7121 (p0) cc_final: 0.6824 (p0) REVERT: G 454 ASP cc_start: 0.6843 (m-30) cc_final: 0.6561 (m-30) REVERT: K 50 ILE cc_start: 0.8148 (mm) cc_final: 0.7825 (mm) REVERT: M 98 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8005 (m) outliers start: 62 outliers final: 52 residues processed: 535 average time/residue: 0.3768 time to fit residues: 296.0441 Evaluate side-chains 554 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 495 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 247 optimal weight: 1.9990 chunk 151 optimal weight: 0.0670 chunk 117 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 207 optimal weight: 0.0040 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN G 195 GLN G 247 ASN G 332 HIS G 346 GLN G 351 ASN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN L 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20928 Z= 0.196 Angle : 0.522 8.195 28386 Z= 0.280 Chirality : 0.044 0.238 3261 Planarity : 0.004 0.035 3618 Dihedral : 5.766 58.634 3166 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.68 % Allowed : 18.30 % Favored : 79.03 % 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: -0.06 (0.17), residues: 2643 helix: 0.73 (0.26), residues: 405 sheet: -0.16 (0.17), residues: 915 loop : -0.04 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 50 HIS 0.004 0.001 HIS C 332 PHE 0.011 0.001 PHE K 101 TYR 0.017 0.001 TYR G 269 ARG 0.005 0.000 ARG F 129 ********************** 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 560 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 500 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7990 (p) REVERT: C 110 CYS cc_start: 0.5144 (OUTLIER) cc_final: 0.4922 (m) REVERT: C 192 SER cc_start: 0.7885 (t) cc_final: 0.7535 (p) REVERT: C 195 GLN cc_start: 0.7456 (mt0) cc_final: 0.7117 (mt0) REVERT: C 318 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8208 (t) REVERT: C 343 VAL cc_start: 0.8448 (p) cc_final: 0.8202 (m) REVERT: C 399 ILE cc_start: 0.7925 (mm) cc_final: 0.7642 (mt) REVERT: D 71 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7367 (pmt-80) REVERT: E 74 THR cc_start: 0.7984 (m) cc_final: 0.7595 (p) REVERT: F 62 ASP cc_start: 0.7083 (m-30) cc_final: 0.6775 (m-30) REVERT: F 133 GLU cc_start: 0.6763 (tp30) cc_final: 0.6295 (tp30) REVERT: F 163 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.6983 (mtm-85) REVERT: F 189 MET cc_start: 0.6664 (mmt) cc_final: 0.6266 (mmt) REVERT: F 343 VAL cc_start: 0.8425 (p) cc_final: 0.8090 (m) REVERT: F 397 VAL cc_start: 0.7697 (t) cc_final: 0.7395 (m) REVERT: G 70 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: G 131 GLU cc_start: 0.6890 (tt0) cc_final: 0.6572 (tt0) REVERT: G 144 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7679 (t) REVERT: G 156 ARG cc_start: 0.7001 (ptm-80) cc_final: 0.6610 (ptt-90) REVERT: G 167 ASP cc_start: 0.6690 (m-30) cc_final: 0.6267 (m-30) REVERT: G 177 ILE cc_start: 0.7610 (mt) cc_final: 0.7383 (mt) REVERT: G 197 ASN cc_start: 0.8239 (p0) cc_final: 0.7708 (p0) REVERT: G 280 ASP cc_start: 0.7103 (t70) cc_final: 0.6811 (t70) REVERT: G 329 ARG cc_start: 0.7393 (ttm110) cc_final: 0.7038 (ttm-80) REVERT: G 343 VAL cc_start: 0.8433 (p) cc_final: 0.8182 (m) REVERT: G 353 ASN cc_start: 0.7112 (p0) cc_final: 0.6822 (p0) REVERT: G 454 ASP cc_start: 0.6833 (m-30) cc_final: 0.6573 (m-30) REVERT: J 74 ASN cc_start: 0.8384 (m-40) cc_final: 0.8182 (m110) REVERT: K 50 ILE cc_start: 0.8139 (mm) cc_final: 0.7819 (mm) outliers start: 60 outliers final: 49 residues processed: 535 average time/residue: 0.3619 time to fit residues: 282.9453 Evaluate side-chains 548 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 493 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 394 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 69 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN G 233 ASN G 247 ASN G 346 GLN G 351 ASN G 412 ASN ** G 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106469 restraints weight = 28234.835| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.76 r_work: 0.3193 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20928 Z= 0.319 Angle : 0.570 8.334 28386 Z= 0.306 Chirality : 0.045 0.235 3261 Planarity : 0.004 0.049 3618 Dihedral : 5.922 57.970 3166 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.77 % Allowed : 18.16 % Favored : 79.07 % 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: -0.18 (0.16), residues: 2643 helix: 0.51 (0.26), residues: 405 sheet: -0.19 (0.17), residues: 906 loop : -0.13 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 37 HIS 0.005 0.001 HIS C 332 PHE 0.019 0.002 PHE J 29 TYR 0.022 0.002 TYR K 51 ARG 0.009 0.000 ARG F 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6075.48 seconds wall clock time: 110 minutes 44.70 seconds (6644.70 seconds total)