Starting phenix.real_space_refine on Tue Aug 26 15:59:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zr4_60391/08_2025/8zr4_60391_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zr4_60391/08_2025/8zr4_60391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zr4_60391/08_2025/8zr4_60391_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zr4_60391/08_2025/8zr4_60391_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zr4_60391/08_2025/8zr4_60391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zr4_60391/08_2025/8zr4_60391.map" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 S 120 5.16 5 C 12269 2.51 5 N 3432 2.21 5 O 4701 1.98 5 H 18458 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38984 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1929 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 3 Chain: "B" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1682 Classifications: {'peptide': 111} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 5866 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 386, 5823 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} Conformer: "B" Number of residues, atoms: 386, 5823 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} bond proxies already assigned to first conformer: 5843 Chain: "F" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1913 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 3 Chain: "G" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "H" Number of atoms: 5866 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 386, 5823 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} Conformer: "B" Number of residues, atoms: 386, 5823 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} bond proxies already assigned to first conformer: 5843 Chain: "I" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1929 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 3 Chain: "J" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "K" Number of atoms: 5866 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 386, 5823 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} Conformer: "B" Number of residues, atoms: 386, 5823 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} bond proxies already assigned to first conformer: 5843 Chain: "L" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1929 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 3 Chain: "M" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1663 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "N" Number of atoms: 5866 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 386, 5823 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} Conformer: "B" Number of residues, atoms: 386, 5823 Classifications: {'peptide': 386} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 371} bond proxies already assigned to first conformer: 5843 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "H" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 164 Classifications: {'water': 164} Link IDs: {None: 163} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "N" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AVAL D 98 " occ=0.41 ... (28 atoms not shown) pdb="HG23BVAL D 98 " occ=0.59 residue: pdb=" N AVAL H 98 " occ=0.26 ... (28 atoms not shown) pdb="HG23BVAL H 98 " occ=0.74 residue: pdb=" N AVAL K 98 " occ=0.40 ... (28 atoms not shown) pdb="HG23BVAL K 98 " occ=0.60 residue: pdb=" N AVAL N 98 " occ=0.44 ... (28 atoms not shown) pdb="HG23BVAL N 98 " occ=0.56 Time building chain proxies: 9.52, per 1000 atoms: 0.24 Number of scatterers: 38984 At special positions: 0 Unit cell: (165.6, 166.52, 78.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 120 16.00 O 4701 8.00 N 3432 7.00 C 12269 6.00 H 18458 1.00 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 341 " distance=2.02 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 53 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 154 " distance=2.04 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 156 " distance=2.07 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 202 " - pdb=" SG CYS D 215 " distance=2.03 Simple disulfide: pdb=" SG CYS D 204 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 261 " distance=2.04 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 371 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 341 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 53 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 117 " distance=2.03 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 154 " distance=2.04 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 156 " distance=2.07 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 161 " distance=2.03 Simple disulfide: pdb=" SG CYS H 202 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS H 204 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 242 " - pdb=" SG CYS H 261 " distance=2.04 Simple disulfide: pdb=" SG CYS H 345 " - pdb=" SG CYS H 371 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 341 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 53 " distance=2.03 Simple disulfide: pdb=" SG CYS K 99 " - pdb=" SG CYS K 117 " distance=2.03 Simple disulfide: pdb=" SG CYS K 107 " - pdb=" SG CYS K 154 " distance=2.04 Simple disulfide: pdb=" SG CYS K 107 " - pdb=" SG CYS K 156 " distance=2.07 Simple disulfide: pdb=" SG CYS K 156 " - pdb=" SG CYS K 161 " distance=2.03 Simple disulfide: pdb=" SG CYS K 202 " - pdb=" SG CYS K 215 " distance=2.03 Simple disulfide: pdb=" SG CYS K 204 " - pdb=" SG CYS K 213 " distance=2.03 Simple disulfide: pdb=" SG CYS K 242 " - pdb=" SG CYS K 261 " distance=2.04 Simple disulfide: pdb=" SG CYS K 345 " - pdb=" SG CYS K 371 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 93 " distance=2.03 Simple disulfide: pdb=" SG CYS N 16 " - pdb=" SG CYS N 341 " distance=2.03 Simple disulfide: pdb=" SG CYS N 48 " - pdb=" SG CYS N 53 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 117 " distance=2.03 Simple disulfide: pdb=" SG CYS N 107 " - pdb=" SG CYS N 154 " distance=2.04 Simple disulfide: pdb=" SG CYS N 107 " - pdb=" SG CYS N 156 " distance=2.07 Simple disulfide: pdb=" SG CYS N 156 " - pdb=" SG CYS N 161 " distance=2.03 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 215 " distance=2.03 Simple disulfide: pdb=" SG CYS N 204 " - pdb=" SG CYS N 213 " distance=2.03 Simple disulfide: pdb=" SG CYS N 242 " - pdb=" SG CYS N 261 " distance=2.04 Simple disulfide: pdb=" SG CYS N 345 " - pdb=" SG CYS N 371 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 52 sheets defined 5.8% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'D' and resid 28 through 34 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'G' and resid 84 through 88 Processing helix chain 'H' and resid 28 through 34 Processing helix chain 'H' and resid 66 through 70 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'J' and resid 84 through 88 Processing helix chain 'K' and resid 28 through 34 Processing helix chain 'K' and resid 66 through 70 Processing helix chain 'K' and resid 387 through 391 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'M' and resid 84 through 88 Processing helix chain 'N' and resid 28 through 34 Processing helix chain 'N' and resid 66 through 70 Processing helix chain 'N' and resid 387 through 391 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.093A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 124 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 5.093A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.609A pdb=" N ASP B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.350A pdb=" N LEU B 38 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR B 54 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.839A pdb=" N THR B 103 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 20 through 26 removed outlier: 5.343A pdb=" N PHE D 21 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR D 373 " --> pdb=" O PHE D 21 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N CYS D 371 " --> pdb=" O PRO D 23 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG D 344 " --> pdb=" O GLY D 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 39 through 48 removed outlier: 4.755A pdb=" N TRP D 39 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR D 62 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR D 41 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN D 60 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU D 43 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU D 58 " --> pdb=" O GLU D 43 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 81 " --> pdb=" O GLY D 59 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU D 82 " --> pdb=" O AVAL D 98 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 108 removed outlier: 4.077A pdb=" N ASP D 121 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 131 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'D' and resid 148 through 149 removed outlier: 6.660A pdb=" N GLU D 182 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 200 through 207 removed outlier: 5.347A pdb=" N GLU D 201 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG D 216 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 277 through 280 removed outlier: 6.995A pdb=" N ASP D 326 " --> pdb=" O GLY D 297 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N GLU D 299 " --> pdb=" O ARG D 324 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ARG D 324 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N PHE D 301 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 13.314A pdb=" N VAL D 322 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 15.511A pdb=" N VAL D 303 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 16.132A pdb=" N VAL D 320 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.094A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL F 124 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.094A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.518A pdb=" N ASP G 75 " --> pdb=" O SER G 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.345A pdb=" N LEU G 38 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR G 54 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP G 40 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.836A pdb=" N THR G 103 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 20 through 26 removed outlier: 5.333A pdb=" N PHE H 21 " --> pdb=" O THR H 373 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR H 373 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N CYS H 371 " --> pdb=" O PRO H 23 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG H 344 " --> pdb=" O GLY H 372 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 39 through 48 removed outlier: 4.751A pdb=" N TRP H 39 " --> pdb=" O THR H 62 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR H 62 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N THR H 41 " --> pdb=" O GLN H 60 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN H 60 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLU H 43 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU H 58 " --> pdb=" O GLU H 43 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR H 81 " --> pdb=" O GLY H 59 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU H 82 " --> pdb=" O AVAL H 98 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS H 96 " --> pdb=" O MET H 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 103 through 108 removed outlier: 3.979A pdb=" N ASP H 121 " --> pdb=" O ASN H 124 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR H 131 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU H 135 " --> pdb=" O TYR H 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 148 through 149 Processing sheet with id=AC6, first strand: chain 'H' and resid 148 through 149 removed outlier: 6.632A pdb=" N GLU H 182 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE H 186 " --> pdb=" O GLU H 182 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 200 through 207 removed outlier: 5.341A pdb=" N GLU H 201 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG H 216 " --> pdb=" O GLU H 201 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 277 through 280 removed outlier: 6.906A pdb=" N ASP H 326 " --> pdb=" O GLY H 297 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLU H 299 " --> pdb=" O ARG H 324 " (cutoff:3.500A) removed outlier: 10.408A pdb=" N ARG H 324 " --> pdb=" O GLU H 299 " (cutoff:3.500A) removed outlier: 11.428A pdb=" N PHE H 301 " --> pdb=" O VAL H 322 " (cutoff:3.500A) removed outlier: 13.318A pdb=" N VAL H 322 " --> pdb=" O PHE H 301 " (cutoff:3.500A) removed outlier: 15.517A pdb=" N VAL H 303 " --> pdb=" O VAL H 320 " (cutoff:3.500A) removed outlier: 16.136A pdb=" N VAL H 320 " --> pdb=" O VAL H 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.099A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL I 124 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.099A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.520A pdb=" N ASP J 75 " --> pdb=" O SER J 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.345A pdb=" N LEU J 38 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR J 54 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP J 40 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.836A pdb=" N THR J 103 " --> pdb=" O GLN J 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 20 through 26 removed outlier: 5.349A pdb=" N PHE K 21 " --> pdb=" O THR K 373 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR K 373 " --> pdb=" O PHE K 21 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N CYS K 371 " --> pdb=" O PRO K 23 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ARG K 344 " --> pdb=" O GLY K 372 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 39 through 48 removed outlier: 4.751A pdb=" N TRP K 39 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR K 62 " --> pdb=" O TRP K 39 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR K 41 " --> pdb=" O GLN K 60 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN K 60 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU K 43 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU K 58 " --> pdb=" O GLU K 43 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR K 81 " --> pdb=" O GLY K 59 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU K 82 " --> pdb=" O AVAL K 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS K 96 " --> pdb=" O MET K 84 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 103 through 108 removed outlier: 4.138A pdb=" N ASP K 121 " --> pdb=" O ASN K 124 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR K 131 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU K 135 " --> pdb=" O TYR K 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 148 through 149 Processing sheet with id=AE1, first strand: chain 'K' and resid 148 through 149 removed outlier: 6.643A pdb=" N GLU K 182 " --> pdb=" O ILE K 186 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE K 186 " --> pdb=" O GLU K 182 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 200 through 207 removed outlier: 5.341A pdb=" N GLU K 201 " --> pdb=" O ARG K 216 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG K 216 " --> pdb=" O GLU K 201 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 277 through 280 removed outlier: 6.916A pdb=" N ASP K 326 " --> pdb=" O GLY K 297 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N GLU K 299 " --> pdb=" O ARG K 324 " (cutoff:3.500A) removed outlier: 10.406A pdb=" N ARG K 324 " --> pdb=" O GLU K 299 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N PHE K 301 " --> pdb=" O VAL K 322 " (cutoff:3.500A) removed outlier: 13.314A pdb=" N VAL K 322 " --> pdb=" O PHE K 301 " (cutoff:3.500A) removed outlier: 15.518A pdb=" N VAL K 303 " --> pdb=" O VAL K 320 " (cutoff:3.500A) removed outlier: 16.138A pdb=" N VAL K 320 " --> pdb=" O VAL K 303 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 58 through 60 removed outlier: 5.099A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL L 124 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 58 through 60 removed outlier: 5.099A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.520A pdb=" N ASP M 75 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.343A pdb=" N LEU M 38 " --> pdb=" O TYR M 54 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR M 54 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP M 40 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.838A pdb=" N THR M 103 " --> pdb=" O GLN M 95 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 20 through 26 removed outlier: 5.332A pdb=" N PHE N 21 " --> pdb=" O THR N 373 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR N 373 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N CYS N 371 " --> pdb=" O PRO N 23 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG N 344 " --> pdb=" O GLY N 372 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 39 through 48 removed outlier: 4.751A pdb=" N TRP N 39 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR N 62 " --> pdb=" O TRP N 39 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR N 41 " --> pdb=" O GLN N 60 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN N 60 " --> pdb=" O THR N 41 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU N 43 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU N 58 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR N 81 " --> pdb=" O GLY N 59 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU N 82 " --> pdb=" O AVAL N 98 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS N 96 " --> pdb=" O MET N 84 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 103 through 108 removed outlier: 4.192A pdb=" N ASP N 121 " --> pdb=" O ASN N 124 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR N 131 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU N 135 " --> pdb=" O TYR N 131 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 148 through 149 Processing sheet with id=AF5, first strand: chain 'N' and resid 148 through 149 removed outlier: 6.616A pdb=" N GLU N 182 " --> pdb=" O ILE N 186 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE N 186 " --> pdb=" O GLU N 182 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 200 through 207 removed outlier: 5.341A pdb=" N GLU N 201 " --> pdb=" O ARG N 216 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG N 216 " --> pdb=" O GLU N 201 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 277 through 280 removed outlier: 6.913A pdb=" N ASP N 326 " --> pdb=" O GLY N 297 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N GLU N 299 " --> pdb=" O ARG N 324 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N ARG N 324 " --> pdb=" O GLU N 299 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N PHE N 301 " --> pdb=" O VAL N 322 " (cutoff:3.500A) removed outlier: 13.316A pdb=" N VAL N 322 " --> pdb=" O PHE N 301 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N VAL N 303 " --> pdb=" O VAL N 320 " (cutoff:3.500A) removed outlier: 16.146A pdb=" N VAL N 320 " --> pdb=" O VAL N 303 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.52 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 18458 1.04 - 1.26: 3232 1.26 - 1.47: 8448 1.47 - 1.68: 8349 1.68 - 1.89: 152 Bond restraints: 38639 Sorted by residual: bond pdb=" N GLY L 2 " pdb=" CA GLY L 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.22e+00 bond pdb=" N GLY F 2 " pdb=" CA GLY F 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.97e+00 bond pdb=" N GLY I 2 " pdb=" CA GLY I 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.96e+00 bond pdb=" N GLY A 2 " pdb=" CA GLY A 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.94e+00 bond pdb=" CB CYS H 156 " pdb=" SG CYS H 156 " ideal model delta sigma weight residual 1.808 1.888 -0.080 3.30e-02 9.18e+02 5.81e+00 ... (remaining 38634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 65936 1.22 - 2.45: 2834 2.45 - 3.67: 249 3.67 - 4.89: 73 4.89 - 6.12: 38 Bond angle restraints: 69130 Sorted by residual: angle pdb=" C ARG D 354 " pdb=" N LYS D 355 " pdb=" CA LYS D 355 " ideal model delta sigma weight residual 121.70 127.20 -5.50 1.80e+00 3.09e-01 9.33e+00 angle pdb=" C ARG H 354 " pdb=" N LYS H 355 " pdb=" CA LYS H 355 " ideal model delta sigma weight residual 121.70 127.16 -5.46 1.80e+00 3.09e-01 9.21e+00 angle pdb=" C ARG K 354 " pdb=" N LYS K 355 " pdb=" CA LYS K 355 " ideal model delta sigma weight residual 121.70 127.11 -5.41 1.80e+00 3.09e-01 9.05e+00 angle pdb=" C ARG N 354 " pdb=" N LYS N 355 " pdb=" CA LYS N 355 " ideal model delta sigma weight residual 121.70 127.11 -5.41 1.80e+00 3.09e-01 9.04e+00 angle pdb=" CA CYS N 107 " pdb=" CB CYS N 107 " pdb=" SG CYS N 107 " ideal model delta sigma weight residual 114.40 120.52 -6.12 2.30e+00 1.89e-01 7.07e+00 ... (remaining 69125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 17470 21.13 - 42.25: 991 42.25 - 63.38: 293 63.38 - 84.50: 63 84.50 - 105.63: 28 Dihedral angle restraints: 18845 sinusoidal: 10393 harmonic: 8452 Sorted by residual: dihedral pdb=" CA CYS D 261 " pdb=" C CYS D 261 " pdb=" N LEU D 262 " pdb=" CA LEU D 262 " ideal model delta harmonic sigma weight residual 180.00 152.15 27.85 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA CYS N 261 " pdb=" C CYS N 261 " pdb=" N LEU N 262 " pdb=" CA LEU N 262 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA CYS K 261 " pdb=" C CYS K 261 " pdb=" N LEU K 262 " pdb=" CA LEU K 262 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 18842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2541 0.055 - 0.109: 379 0.109 - 0.164: 112 0.164 - 0.219: 0 0.219 - 0.274: 4 Chirality restraints: 3036 Sorted by residual: chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 3033 not shown) Planarity restraints: 5856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 43 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO K 44 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO K 44 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO K 44 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 43 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO H 44 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 44 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 44 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 43 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO D 44 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 44 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 44 " -0.021 5.00e-02 4.00e+02 ... (remaining 5853 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1714 2.12 - 2.74: 71268 2.74 - 3.36: 124417 3.36 - 3.98: 174570 3.98 - 4.60: 259759 Nonbonded interactions: 631728 Sorted by model distance: nonbonded pdb=" OE1 GLN K 15 " pdb=" HE ARG K 344 " model vdw 1.496 2.450 nonbonded pdb=" O VAL N 304 " pdb=" HG SER N 312 " model vdw 1.517 2.450 nonbonded pdb=" OE1 GLN D 15 " pdb=" HE ARG D 344 " model vdw 1.543 2.450 nonbonded pdb=" OE1 GLN H 15 " pdb=" HE ARG H 344 " model vdw 1.569 2.450 nonbonded pdb=" OE1 GLN N 15 " pdb=" HE ARG N 344 " model vdw 1.583 2.450 ... (remaining 631723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 132) selection = chain 'F' selection = (chain 'I' and resid 2 through 132) selection = (chain 'L' and resid 2 through 132) } ncs_group { reference = (chain 'B' and resid 2 through 111) selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = (chain 'D' and (resid 6 through 97 or resid 99 through 145 or resid 147 through \ 366 or resid 368 through 403)) selection = (chain 'H' and (resid 6 through 97 or resid 99 through 145 or resid 147 through \ 366 or resid 368 through 403)) selection = (chain 'K' and (resid 6 through 97 or resid 99 through 145 or resid 147 through \ 366 or resid 368 through 403)) selection = (chain 'N' and (resid 6 through 97 or resid 99 through 145 or resid 147 through \ 366 or resid 368 through 403)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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=0.25 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.340 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 38.490 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 0.080 20245 Z= 0.170 Angle : 0.672 10.835 27537 Z= 0.341 Chirality : 0.046 0.274 3036 Planarity : 0.004 0.038 3496 Dihedral : 15.413 105.625 7657 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.60 % Allowed : 8.22 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.17), residues: 2460 helix: 0.62 (0.86), residues: 24 sheet: -0.54 (0.16), residues: 889 loop : 0.02 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.015 0.002 TYR D 45 PHE 0.011 0.001 PHE D 278 TRP 0.018 0.002 TRP N 102 HIS 0.004 0.001 HIS H 115 Details of bonding type rmsd covalent geometry : bond 0.00352 (20181) covalent geometry : angle 0.64468 (27393) SS BOND : bond 0.01117 ( 48) SS BOND : angle 2.95199 ( 96) hydrogen bonds : bond 0.21135 ( 688) hydrogen bonds : angle 9.45828 ( 1908) link_ALPHA1-3 : bond 0.00045 ( 4) link_ALPHA1-3 : angle 2.18804 ( 12) link_ALPHA1-6 : bond 0.00375 ( 4) link_ALPHA1-6 : angle 1.80601 ( 12) link_BETA1-4 : bond 0.01126 ( 8) link_BETA1-4 : angle 2.30972 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 323 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 335 average time/residue: 1.3072 time to fit residues: 494.8012 Evaluate side-chains 327 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 316 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 GLN F 84 ASN I 84 ASN L 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.168940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.149311 restraints weight = 43005.192| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 0.50 r_work: 0.3397 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work: 0.3135 rms_B_bonded: 4.48 restraints_weight: 0.1250 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 20245 Z= 0.284 Angle : 0.805 16.109 27537 Z= 0.433 Chirality : 0.049 0.181 3036 Planarity : 0.005 0.043 3496 Dihedral : 10.330 80.743 3311 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.74 % Allowed : 7.85 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.16), residues: 2460 helix: -1.92 (0.47), residues: 24 sheet: -0.59 (0.16), residues: 870 loop : -0.19 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 80 TYR 0.021 0.003 TYR K 45 PHE 0.010 0.002 PHE D 334 TRP 0.021 0.003 TRP K 102 HIS 0.008 0.002 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00553 (20181) covalent geometry : angle 0.76432 (27393) SS BOND : bond 0.02314 ( 48) SS BOND : angle 4.08462 ( 96) hydrogen bonds : bond 0.07494 ( 688) hydrogen bonds : angle 7.79353 ( 1908) link_ALPHA1-3 : bond 0.00078 ( 4) link_ALPHA1-3 : angle 2.68373 ( 12) link_ALPHA1-6 : bond 0.00332 ( 4) link_ALPHA1-6 : angle 1.66512 ( 12) link_BETA1-4 : bond 0.01043 ( 8) link_BETA1-4 : angle 2.30624 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 320 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 292 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6959 (mt-10) REVERT: L 84 ASN cc_start: 0.8117 (m-40) cc_final: 0.7791 (m-40) outliers start: 16 outliers final: 9 residues processed: 335 average time/residue: 1.3061 time to fit residues: 494.0079 Evaluate side-chains 323 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 314 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 14 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN F 84 ASN I 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.170774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.151105 restraints weight = 50803.978| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 0.55 r_work: 0.3410 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work: 0.3144 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 20245 Z= 0.231 Angle : 0.746 14.747 27537 Z= 0.401 Chirality : 0.048 0.193 3036 Planarity : 0.005 0.040 3496 Dihedral : 9.939 75.697 3304 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.51 % Allowed : 8.50 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.16), residues: 2460 helix: -1.95 (0.54), residues: 24 sheet: -0.83 (0.15), residues: 911 loop : -0.15 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 9 TYR 0.020 0.002 TYR K 45 PHE 0.016 0.002 PHE H 334 TRP 0.019 0.002 TRP K 102 HIS 0.006 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00455 (20181) covalent geometry : angle 0.70848 (27393) SS BOND : bond 0.01866 ( 48) SS BOND : angle 3.77319 ( 96) hydrogen bonds : bond 0.06479 ( 688) hydrogen bonds : angle 7.32411 ( 1908) link_ALPHA1-3 : bond 0.00341 ( 4) link_ALPHA1-3 : angle 2.34211 ( 12) link_ALPHA1-6 : bond 0.00441 ( 4) link_ALPHA1-6 : angle 1.53536 ( 12) link_BETA1-4 : bond 0.00907 ( 8) link_BETA1-4 : angle 2.33604 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 320 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7995 (m-40) cc_final: 0.7739 (m-40) REVERT: B 50 GLN cc_start: 0.8773 (pt0) cc_final: 0.8469 (pt0) REVERT: F 84 ASN cc_start: 0.8060 (m-40) cc_final: 0.7771 (m-40) REVERT: G 50 GLN cc_start: 0.8819 (pt0) cc_final: 0.8521 (pt0) REVERT: J 50 GLN cc_start: 0.8807 (pt0) cc_final: 0.8514 (pt0) REVERT: N 312 SER cc_start: 0.8339 (t) cc_final: 0.8063 (p) outliers start: 11 outliers final: 11 residues processed: 329 average time/residue: 1.2710 time to fit residues: 473.1571 Evaluate side-chains 312 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 301 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 215 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 GLN L 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.170542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.150414 restraints weight = 49330.876| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 0.54 r_work: 0.3405 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work: 0.3141 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 20245 Z= 0.235 Angle : 0.749 14.931 27537 Z= 0.401 Chirality : 0.048 0.186 3036 Planarity : 0.005 0.040 3496 Dihedral : 9.936 75.261 3304 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.56 % Allowed : 8.41 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.16), residues: 2460 helix: -2.04 (0.52), residues: 24 sheet: -0.85 (0.15), residues: 911 loop : -0.14 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 251 TYR 0.020 0.002 TYR H 45 PHE 0.014 0.002 PHE N 334 TRP 0.019 0.002 TRP K 102 HIS 0.006 0.001 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00463 (20181) covalent geometry : angle 0.71171 (27393) SS BOND : bond 0.01889 ( 48) SS BOND : angle 3.74838 ( 96) hydrogen bonds : bond 0.06268 ( 688) hydrogen bonds : angle 7.22807 ( 1908) link_ALPHA1-3 : bond 0.00243 ( 4) link_ALPHA1-3 : angle 2.50207 ( 12) link_ALPHA1-6 : bond 0.00478 ( 4) link_ALPHA1-6 : angle 1.45144 ( 12) link_BETA1-4 : bond 0.00948 ( 8) link_BETA1-4 : angle 2.36212 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 316 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8032 (m-40) cc_final: 0.7750 (m-40) REVERT: B 50 GLN cc_start: 0.8768 (pt0) cc_final: 0.8464 (pt0) REVERT: F 84 ASN cc_start: 0.8143 (m-40) cc_final: 0.7827 (m-40) REVERT: L 84 ASN cc_start: 0.8084 (m-40) cc_final: 0.7763 (m-40) REVERT: N 312 SER cc_start: 0.8365 (t) cc_final: 0.8090 (p) outliers start: 12 outliers final: 10 residues processed: 327 average time/residue: 1.3164 time to fit residues: 486.9248 Evaluate side-chains 319 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 309 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 124 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 GLN I 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149868 restraints weight = 42935.794| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 0.50 r_work: 0.3370 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.3139 rms_B_bonded: 4.18 restraints_weight: 0.1250 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 20245 Z= 0.264 Angle : 0.782 16.020 27537 Z= 0.418 Chirality : 0.048 0.177 3036 Planarity : 0.005 0.043 3496 Dihedral : 10.097 77.099 3304 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.93 % Allowed : 8.13 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.16), residues: 2460 helix: -2.18 (0.49), residues: 24 sheet: -0.82 (0.15), residues: 911 loop : -0.19 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 251 TYR 0.021 0.003 TYR H 45 PHE 0.014 0.002 PHE D 334 TRP 0.019 0.002 TRP D 102 HIS 0.007 0.002 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00517 (20181) covalent geometry : angle 0.74190 (27393) SS BOND : bond 0.02150 ( 48) SS BOND : angle 3.97060 ( 96) hydrogen bonds : bond 0.06544 ( 688) hydrogen bonds : angle 7.27624 ( 1908) link_ALPHA1-3 : bond 0.00113 ( 4) link_ALPHA1-3 : angle 2.53621 ( 12) link_ALPHA1-6 : bond 0.00466 ( 4) link_ALPHA1-6 : angle 1.47978 ( 12) link_BETA1-4 : bond 0.01055 ( 8) link_BETA1-4 : angle 2.36753 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 310 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8105 (m-40) cc_final: 0.7785 (m-40) REVERT: B 50 GLN cc_start: 0.8755 (pt0) cc_final: 0.8444 (pt0) REVERT: F 84 ASN cc_start: 0.8154 (m-40) cc_final: 0.7844 (m-40) REVERT: I 34 MET cc_start: 0.8943 (mmm) cc_final: 0.8646 (mmm) REVERT: I 84 ASN cc_start: 0.8076 (m-40) cc_final: 0.7680 (m-40) REVERT: L 34 MET cc_start: 0.8954 (mmm) cc_final: 0.8661 (mmm) REVERT: L 84 ASN cc_start: 0.8113 (m-40) cc_final: 0.7796 (m-40) REVERT: N 10 ASN cc_start: 0.8687 (p0) cc_final: 0.8477 (m-40) REVERT: N 312 SER cc_start: 0.8377 (t) cc_final: 0.8103 (p) outliers start: 20 outliers final: 10 residues processed: 328 average time/residue: 1.2927 time to fit residues: 479.7384 Evaluate side-chains 318 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 308 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 68 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 134 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.172576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.153078 restraints weight = 49732.029| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 0.55 r_work: 0.3438 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work: 0.3192 rms_B_bonded: 4.41 restraints_weight: 0.1250 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 20245 Z= 0.187 Angle : 0.693 12.994 27537 Z= 0.371 Chirality : 0.047 0.195 3036 Planarity : 0.004 0.037 3496 Dihedral : 9.525 71.828 3304 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.70 % Allowed : 8.22 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.16), residues: 2460 helix: -1.80 (0.62), residues: 24 sheet: -0.90 (0.15), residues: 895 loop : -0.14 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 9 TYR 0.019 0.002 TYR H 45 PHE 0.014 0.001 PHE N 334 TRP 0.017 0.002 TRP N 102 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00380 (20181) covalent geometry : angle 0.65785 (27393) SS BOND : bond 0.01566 ( 48) SS BOND : angle 3.46632 ( 96) hydrogen bonds : bond 0.05556 ( 688) hydrogen bonds : angle 7.02206 ( 1908) link_ALPHA1-3 : bond 0.00572 ( 4) link_ALPHA1-3 : angle 2.24493 ( 12) link_ALPHA1-6 : bond 0.00532 ( 4) link_ALPHA1-6 : angle 1.47320 ( 12) link_BETA1-4 : bond 0.00745 ( 8) link_BETA1-4 : angle 2.35878 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 316 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8122 (m-40) cc_final: 0.7811 (m-40) REVERT: B 50 GLN cc_start: 0.8735 (pt0) cc_final: 0.8401 (pt0) REVERT: F 84 ASN cc_start: 0.8206 (m-40) cc_final: 0.7896 (m-40) REVERT: G 50 GLN cc_start: 0.8768 (pt0) cc_final: 0.8443 (pt0) REVERT: I 84 ASN cc_start: 0.8059 (m-40) cc_final: 0.7696 (m-40) REVERT: J 50 GLN cc_start: 0.8761 (pt0) cc_final: 0.8436 (pt0) REVERT: L 84 ASN cc_start: 0.8153 (m-40) cc_final: 0.7844 (m-40) REVERT: M 50 GLN cc_start: 0.8735 (pt0) cc_final: 0.8406 (pt0) REVERT: N 10 ASN cc_start: 0.8665 (p0) cc_final: 0.8452 (m-40) REVERT: N 312 SER cc_start: 0.8391 (t) cc_final: 0.8125 (p) outliers start: 15 outliers final: 11 residues processed: 328 average time/residue: 1.3165 time to fit residues: 488.6765 Evaluate side-chains 319 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 308 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 65 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 170 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN I 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.168376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.148038 restraints weight = 52329.242| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 0.64 r_work: 0.3334 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.144 20245 Z= 0.350 Angle : 0.889 18.362 27537 Z= 0.474 Chirality : 0.050 0.243 3036 Planarity : 0.006 0.046 3496 Dihedral : 10.593 82.755 3304 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.56 % Allowed : 8.92 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.16), residues: 2460 helix: -2.32 (0.44), residues: 24 sheet: -0.74 (0.15), residues: 901 loop : -0.29 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 251 TYR 0.022 0.004 TYR N 45 PHE 0.013 0.003 PHE D 334 TRP 0.021 0.003 TRP N 102 HIS 0.011 0.002 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00684 (20181) covalent geometry : angle 0.84125 (27393) SS BOND : bond 0.02791 ( 48) SS BOND : angle 4.66777 ( 96) hydrogen bonds : bond 0.07254 ( 688) hydrogen bonds : angle 7.42288 ( 1908) link_ALPHA1-3 : bond 0.00238 ( 4) link_ALPHA1-3 : angle 2.59763 ( 12) link_ALPHA1-6 : bond 0.00457 ( 4) link_ALPHA1-6 : angle 1.53858 ( 12) link_BETA1-4 : bond 0.01403 ( 8) link_BETA1-4 : angle 2.52631 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 317 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 34 MET cc_start: 0.8903 (mmm) cc_final: 0.8557 (mmm) REVERT: I 82 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7456 (tm130) REVERT: K 165 MET cc_start: 0.8725 (mtp) cc_final: 0.8200 (ttm) REVERT: L 34 MET cc_start: 0.8930 (mmm) cc_final: 0.8597 (mmm) REVERT: N 165 MET cc_start: 0.8744 (mtp) cc_final: 0.8224 (ttm) REVERT: N 312 SER cc_start: 0.8385 (t) cc_final: 0.8116 (p) outliers start: 12 outliers final: 10 residues processed: 329 average time/residue: 1.3747 time to fit residues: 510.5983 Evaluate side-chains 324 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 313 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 45 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 222 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN F 84 ASN L 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.150858 restraints weight = 48036.557| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 0.52 r_work: 0.3418 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 20245 Z= 0.221 Angle : 0.736 9.861 27537 Z= 0.395 Chirality : 0.048 0.189 3036 Planarity : 0.005 0.041 3496 Dihedral : 9.934 74.941 3304 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.56 % Allowed : 9.20 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.16), residues: 2460 helix: -1.98 (0.57), residues: 24 sheet: -0.81 (0.15), residues: 919 loop : -0.17 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 251 TYR 0.021 0.002 TYR N 45 PHE 0.013 0.002 PHE H 334 TRP 0.019 0.002 TRP N 102 HIS 0.005 0.001 HIS K 79 Details of bonding type rmsd covalent geometry : bond 0.00434 (20181) covalent geometry : angle 0.70554 (27393) SS BOND : bond 0.01868 ( 48) SS BOND : angle 3.32127 ( 96) hydrogen bonds : bond 0.06075 ( 688) hydrogen bonds : angle 7.17125 ( 1908) link_ALPHA1-3 : bond 0.00330 ( 4) link_ALPHA1-3 : angle 2.46416 ( 12) link_ALPHA1-6 : bond 0.00478 ( 4) link_ALPHA1-6 : angle 1.45914 ( 12) link_BETA1-4 : bond 0.00868 ( 8) link_BETA1-4 : angle 2.35329 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 310 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7962 (m-40) cc_final: 0.7645 (m-40) REVERT: B 50 GLN cc_start: 0.8579 (pt0) cc_final: 0.8262 (pt0) REVERT: F 84 ASN cc_start: 0.8006 (m-40) cc_final: 0.7680 (m-40) REVERT: I 34 MET cc_start: 0.8910 (mmm) cc_final: 0.8566 (mmm) REVERT: I 84 ASN cc_start: 0.7888 (m-40) cc_final: 0.7677 (m-40) REVERT: K 165 MET cc_start: 0.8755 (mtp) cc_final: 0.8205 (ttm) REVERT: L 34 MET cc_start: 0.8936 (mmm) cc_final: 0.8604 (mmm) REVERT: L 84 ASN cc_start: 0.8006 (m-40) cc_final: 0.7681 (m-40) REVERT: N 165 MET cc_start: 0.8758 (mtp) cc_final: 0.8210 (ttm) REVERT: N 312 SER cc_start: 0.8390 (t) cc_final: 0.8129 (p) outliers start: 12 outliers final: 11 residues processed: 321 average time/residue: 1.2717 time to fit residues: 461.1074 Evaluate side-chains 316 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 305 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.168701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.153065 restraints weight = 46993.914| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 0.44 r_work: 0.3448 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3161 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 20245 Z= 0.328 Angle : 0.860 12.906 27537 Z= 0.460 Chirality : 0.050 0.254 3036 Planarity : 0.006 0.048 3496 Dihedral : 10.468 80.900 3304 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.56 % Allowed : 9.25 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.16), residues: 2460 helix: -2.32 (0.45), residues: 24 sheet: -0.65 (0.16), residues: 891 loop : -0.27 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 251 TYR 0.021 0.003 TYR N 45 PHE 0.012 0.003 PHE H 334 TRP 0.021 0.003 TRP D 102 HIS 0.010 0.002 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00637 (20181) covalent geometry : angle 0.82384 (27393) SS BOND : bond 0.02659 ( 48) SS BOND : angle 4.00986 ( 96) hydrogen bonds : bond 0.07132 ( 688) hydrogen bonds : angle 7.40016 ( 1908) link_ALPHA1-3 : bond 0.00134 ( 4) link_ALPHA1-3 : angle 2.60390 ( 12) link_ALPHA1-6 : bond 0.00419 ( 4) link_ALPHA1-6 : angle 1.50982 ( 12) link_BETA1-4 : bond 0.01259 ( 8) link_BETA1-4 : angle 2.40083 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 315 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8107 (m-40) cc_final: 0.7782 (m-40) REVERT: F 84 ASN cc_start: 0.8144 (m-40) cc_final: 0.7804 (m-40) REVERT: I 34 MET cc_start: 0.8991 (mmm) cc_final: 0.8647 (mmm) REVERT: I 84 ASN cc_start: 0.8079 (m-40) cc_final: 0.7845 (m-40) REVERT: L 34 MET cc_start: 0.8997 (mmm) cc_final: 0.8670 (mmm) REVERT: L 84 ASN cc_start: 0.8142 (m-40) cc_final: 0.7819 (m-40) REVERT: N 312 SER cc_start: 0.8490 (t) cc_final: 0.8198 (p) outliers start: 12 outliers final: 11 residues processed: 326 average time/residue: 1.3494 time to fit residues: 498.0166 Evaluate side-chains 326 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 315 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.173033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.153781 restraints weight = 47838.182| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 0.55 r_work: 0.3429 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work: 0.3191 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20245 Z= 0.173 Angle : 0.676 7.751 27537 Z= 0.362 Chirality : 0.047 0.167 3036 Planarity : 0.004 0.039 3496 Dihedral : 9.428 70.320 3304 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.42 % Allowed : 9.57 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.16), residues: 2460 helix: -1.75 (0.63), residues: 24 sheet: -0.87 (0.15), residues: 895 loop : -0.14 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 9 TYR 0.020 0.002 TYR H 45 PHE 0.015 0.001 PHE H 334 TRP 0.017 0.002 TRP H 102 HIS 0.004 0.001 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00341 (20181) covalent geometry : angle 0.65250 (27393) SS BOND : bond 0.01453 ( 48) SS BOND : angle 2.69281 ( 96) hydrogen bonds : bond 0.05361 ( 688) hydrogen bonds : angle 6.95988 ( 1908) link_ALPHA1-3 : bond 0.00631 ( 4) link_ALPHA1-3 : angle 2.25152 ( 12) link_ALPHA1-6 : bond 0.00580 ( 4) link_ALPHA1-6 : angle 1.46071 ( 12) link_BETA1-4 : bond 0.00738 ( 8) link_BETA1-4 : angle 2.34458 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 305 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8108 (m-40) cc_final: 0.7747 (m-40) REVERT: B 50 GLN cc_start: 0.8736 (pt0) cc_final: 0.8402 (pt0) REVERT: F 84 ASN cc_start: 0.8175 (m-40) cc_final: 0.7847 (m-40) REVERT: G 50 GLN cc_start: 0.8764 (pt0) cc_final: 0.8440 (pt0) REVERT: I 34 MET cc_start: 0.8964 (mmm) cc_final: 0.8643 (mmm) REVERT: I 84 ASN cc_start: 0.8065 (m-40) cc_final: 0.7841 (m-40) REVERT: J 50 GLN cc_start: 0.8763 (pt0) cc_final: 0.8438 (pt0) REVERT: K 165 MET cc_start: 0.8883 (mtp) cc_final: 0.8484 (ttm) REVERT: L 34 MET cc_start: 0.8974 (mmm) cc_final: 0.8662 (mmm) REVERT: L 84 ASN cc_start: 0.8124 (m-40) cc_final: 0.7806 (m-40) REVERT: M 50 GLN cc_start: 0.8743 (pt0) cc_final: 0.8418 (pt0) REVERT: N 165 MET cc_start: 0.8880 (mtp) cc_final: 0.8362 (ttm) REVERT: N 312 SER cc_start: 0.8452 (t) cc_final: 0.8182 (p) outliers start: 9 outliers final: 9 residues processed: 314 average time/residue: 1.3202 time to fit residues: 469.4754 Evaluate side-chains 310 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 301 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain N residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.171807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.152212 restraints weight = 45194.982| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 0.51 r_work: 0.3416 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work: 0.3174 rms_B_bonded: 4.36 restraints_weight: 0.1250 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 20245 Z= 0.204 Angle : 0.706 8.917 27537 Z= 0.377 Chirality : 0.047 0.177 3036 Planarity : 0.004 0.038 3496 Dihedral : 9.601 72.522 3303 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.51 % Allowed : 9.43 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.73 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.16), residues: 2460 helix: -1.94 (0.57), residues: 24 sheet: -0.88 (0.15), residues: 895 loop : -0.12 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 9 TYR 0.020 0.002 TYR N 45 PHE 0.013 0.002 PHE D 334 TRP 0.019 0.002 TRP N 102 HIS 0.005 0.001 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00401 (20181) covalent geometry : angle 0.67982 (27393) SS BOND : bond 0.01657 ( 48) SS BOND : angle 2.97574 ( 96) hydrogen bonds : bond 0.05712 ( 688) hydrogen bonds : angle 7.00113 ( 1908) link_ALPHA1-3 : bond 0.00443 ( 4) link_ALPHA1-3 : angle 2.32259 ( 12) link_ALPHA1-6 : bond 0.00480 ( 4) link_ALPHA1-6 : angle 1.45738 ( 12) link_BETA1-4 : bond 0.00846 ( 8) link_BETA1-4 : angle 2.34487 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17498.32 seconds wall clock time: 296 minutes 15.28 seconds (17775.28 seconds total)