Starting phenix.real_space_refine on Mon Jul 6 19:31:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zr4_60391/07_2026/8zr4_60391_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zr4_60391/07_2026/8zr4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zr4_60391/07_2026/8zr4_60391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zr4_60391/07_2026/8zr4_60391.map" model { file = "/net/cci-nas-00/data/ceres_data/8zr4_60391/07_2026/8zr4_60391_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zr4_60391/07_2026/8zr4_60391_trim.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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: 10.70, per 1000 atoms: 0.27 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: 3.93 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.12 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: 13.83 Time building geometry restraints manager: 5.62 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.360 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 49.350 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 are 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/Z covalent geometry : bond 0.00352 / 0.17 (20181) covalent geometry : angle 0.64468 / 0.33 (27393) SS BOND : bond 0.01117 / 0.77 ( 48) SS BOND : angle 2.95199 / 2.30 ( 96) hydrogen bonds : bond 0.21135 / 13.97 ( 688) hydrogen bonds : angle 9.45828 / 6.53 ( 1908) link_ALPHA1-3 : bond 0.00045 / 0.03 ( 4) link_ALPHA1-3 : angle 2.18804 / 1.28 ( 12) link_ALPHA1-6 : bond 0.00375 / 0.23 ( 4) link_ALPHA1-6 : angle 1.80601 / 1.04 ( 12) link_BETA1-4 : bond 0.01126 / 0.76 ( 8) link_BETA1-4 : angle 2.30972 / 1.35 ( 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 : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 335 average time/residue: 1.3407 time to fit residues: 510.0633 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 : 1.081 ------------------------------------------------------------------------------- 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... 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 = 0.3824 r_free = 0.3824 target = 0.169291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149657 restraints weight = 42949.290| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 0.49 r_work: 0.3402 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work: 0.3155 rms_B_bonded: 4.07 restraints_weight: 0.1250 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 20245 Z= 0.286 Angle : 0.807 16.154 27537 Z= 0.435 Chirality : 0.049 0.181 3036 Planarity : 0.005 0.043 3496 Dihedral : 10.315 80.794 3311 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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 are not related in a simple way. whole: -0.61 (0.16), residues: 2460 helix: -1.94 (0.48), residues: 24 sheet: -0.54 (0.16), residues: 862 loop : -0.22 (0.16), residues: 1574 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 K 334 TRP 0.021 0.003 TRP N 102 HIS 0.008 0.002 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.28 (20181) covalent geometry : angle 0.76660 / 0.42 (27393) SS BOND : bond 0.02294 / 1.58 ( 48) SS BOND : angle 4.09023 / 3.16 ( 96) hydrogen bonds : bond 0.07414 / 4.84 ( 688) hydrogen bonds : angle 7.80763 / 5.41 ( 1908) link_ALPHA1-3 : bond 0.00087 / 0.05 ( 4) link_ALPHA1-3 : angle 2.70998 / 1.46 ( 12) link_ALPHA1-6 : bond 0.00335 / 0.21 ( 4) link_ALPHA1-6 : angle 1.70189 / 0.97 ( 12) link_BETA1-4 : bond 0.01060 / 0.70 ( 8) link_BETA1-4 : angle 2.31158 / 1.43 ( 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 335 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 319 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 84 ASN cc_start: 0.8108 (m-40) cc_final: 0.7785 (m-40) outliers start: 16 outliers final: 9 residues processed: 334 average time/residue: 1.2688 time to fit residues: 483.4124 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 : 0.954 ------------------------------------------------------------------------------- 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: 0.9980 chunk 217 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3859 r_free = 0.3859 target = 0.172618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.152279 restraints weight = 51133.534| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 0.60 r_work: 0.3395 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0819 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= 0.190 Angle : 0.696 12.959 27537 Z= 0.374 Chirality : 0.047 0.180 3036 Planarity : 0.004 0.036 3496 Dihedral : 9.581 72.719 3304 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.51 % Allowed : 8.27 % Favored : 91.22 % 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 are not related in a simple way. whole: -0.73 (0.16), residues: 2460 helix: -1.72 (0.61), residues: 24 sheet: -0.84 (0.15), residues: 887 loop : -0.13 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 9 TYR 0.018 0.002 TYR K 45 PHE 0.015 0.001 PHE D 334 TRP 0.017 0.002 TRP K 102 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (20181) covalent geometry : angle 0.66426 / 0.36 (27393) SS BOND : bond 0.01524 / 1.04 ( 48) SS BOND : angle 3.30505 / 2.52 ( 96) hydrogen bonds : bond 0.05988 / 3.90 ( 688) hydrogen bonds : angle 7.22880 / 5.00 ( 1908) link_ALPHA1-3 : bond 0.00561 / 0.35 ( 4) link_ALPHA1-3 : angle 2.21704 / 1.18 ( 12) link_ALPHA1-6 : bond 0.00520 / 0.32 ( 4) link_ALPHA1-6 : angle 1.46966 / 0.85 ( 12) link_BETA1-4 : bond 0.00754 / 0.50 ( 8) link_BETA1-4 : angle 2.30414 / 1.47 ( 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 334 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 323 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7932 (m-40) cc_final: 0.7686 (m-40) REVERT: B 50 GLN cc_start: 0.8598 (pt0) cc_final: 0.8307 (pt0) REVERT: F 84 ASN cc_start: 0.7973 (m-40) cc_final: 0.7705 (m-40) REVERT: G 50 GLN cc_start: 0.8644 (pt0) cc_final: 0.8356 (pt0) REVERT: J 50 GLN cc_start: 0.8642 (pt0) cc_final: 0.8358 (pt0) REVERT: M 50 GLN cc_start: 0.8609 (pt0) cc_final: 0.8319 (pt0) outliers start: 11 outliers final: 11 residues processed: 332 average time/residue: 1.2453 time to fit residues: 471.2934 Evaluate side-chains 309 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 298 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 0.0370 chunk 110 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 84 ASN L 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.171490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.151124 restraints weight = 49366.611| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 0.54 r_work: 0.3420 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work: 0.3160 rms_B_bonded: 4.48 restraints_weight: 0.1250 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 20245 Z= 0.215 Angle : 0.722 14.114 27537 Z= 0.385 Chirality : 0.047 0.180 3036 Planarity : 0.004 0.036 3496 Dihedral : 9.724 73.880 3304 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.56 % Allowed : 8.46 % 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 are not related in a simple way. whole: -0.73 (0.16), residues: 2460 helix: -1.88 (0.56), residues: 24 sheet: -0.88 (0.15), residues: 887 loop : -0.10 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 9 TYR 0.020 0.002 TYR N 45 PHE 0.015 0.002 PHE N 334 TRP 0.017 0.002 TRP N 102 HIS 0.006 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (20181) covalent geometry : angle 0.68657 / 0.37 (27393) SS BOND : bond 0.01742 / 1.20 ( 48) SS BOND : angle 3.54924 / 2.71 ( 96) hydrogen bonds : bond 0.05967 / 3.88 ( 688) hydrogen bonds : angle 7.12486 / 4.92 ( 1908) link_ALPHA1-3 : bond 0.00342 / 0.21 ( 4) link_ALPHA1-3 : angle 2.48505 / 1.33 ( 12) link_ALPHA1-6 : bond 0.00525 / 0.32 ( 4) link_ALPHA1-6 : angle 1.43619 / 0.83 ( 12) link_BETA1-4 : bond 0.00864 / 0.57 ( 8) link_BETA1-4 : angle 2.35967 / 1.48 ( 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 333 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 321 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8020 (m-40) cc_final: 0.7742 (m-40) REVERT: B 50 GLN cc_start: 0.8785 (pt0) cc_final: 0.8448 (pt0) REVERT: F 84 ASN cc_start: 0.8116 (m-40) cc_final: 0.7813 (m-40) REVERT: G 50 GLN cc_start: 0.8795 (pt0) cc_final: 0.8456 (pt0) REVERT: H 165 MET cc_start: 0.8873 (mtp) cc_final: 0.8460 (ttm) REVERT: J 50 GLN cc_start: 0.8788 (pt0) cc_final: 0.8454 (pt0) REVERT: K 165 MET cc_start: 0.8866 (mtp) cc_final: 0.8450 (ttm) REVERT: L 84 ASN cc_start: 0.8083 (m-40) cc_final: 0.7758 (m-40) REVERT: M 50 GLN cc_start: 0.8754 (pt0) cc_final: 0.8411 (pt0) REVERT: N 165 MET cc_start: 0.8862 (mtp) cc_final: 0.8305 (ttm) REVERT: N 312 SER cc_start: 0.8378 (t) cc_final: 0.8100 (p) outliers start: 12 outliers final: 11 residues processed: 331 average time/residue: 1.2360 time to fit residues: 467.0046 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 : 1.103 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 124 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 84 ASN J 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.170986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.152650 restraints weight = 42971.306| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 0.47 r_work: 0.3454 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work: 0.3190 rms_B_bonded: 4.26 restraints_weight: 0.1250 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1009 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= 0.237 Angle : 0.742 14.966 27537 Z= 0.398 Chirality : 0.047 0.170 3036 Planarity : 0.005 0.039 3496 Dihedral : 9.879 75.165 3304 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.93 % Allowed : 8.09 % 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 are not related in a simple way. whole: -0.70 (0.16), residues: 2460 helix: -2.05 (0.53), residues: 24 sheet: -0.81 (0.15), residues: 911 loop : -0.09 (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 K 45 PHE 0.014 0.002 PHE N 334 TRP 0.018 0.002 TRP N 102 HIS 0.006 0.002 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 (20181) covalent geometry : angle 0.70778 / 0.38 (27393) SS BOND : bond 0.01924 / 1.32 ( 48) SS BOND : angle 3.57050 / 2.77 ( 96) hydrogen bonds : bond 0.06201 / 4.03 ( 688) hydrogen bonds : angle 7.16432 / 4.94 ( 1908) link_ALPHA1-3 : bond 0.00238 / 0.15 ( 4) link_ALPHA1-3 : angle 2.48905 / 1.34 ( 12) link_ALPHA1-6 : bond 0.00463 / 0.29 ( 4) link_ALPHA1-6 : angle 1.48474 / 0.86 ( 12) link_BETA1-4 : bond 0.00957 / 0.63 ( 8) link_BETA1-4 : angle 2.34726 / 1.49 ( 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 335 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8095 (m-40) cc_final: 0.7803 (m-40) REVERT: B 50 GLN cc_start: 0.8754 (pt0) cc_final: 0.8423 (pt0) REVERT: F 84 ASN cc_start: 0.8133 (m-40) cc_final: 0.7842 (m-40) REVERT: G 50 GLN cc_start: 0.8772 (pt0) cc_final: 0.8442 (pt0) REVERT: J 50 GLN cc_start: 0.8772 (pt0) cc_final: 0.8448 (pt0) REVERT: L 84 ASN cc_start: 0.8136 (m-40) cc_final: 0.7823 (m-40) REVERT: M 50 GLN cc_start: 0.8736 (pt0) cc_final: 0.8405 (pt0) REVERT: N 312 SER cc_start: 0.8421 (t) cc_final: 0.8155 (p) outliers start: 20 outliers final: 12 residues processed: 331 average time/residue: 1.2976 time to fit residues: 491.8533 Evaluate side-chains 320 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 308 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 126 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 134 optimal weight: 0.0970 chunk 29 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 82 GLN J 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.172686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.153057 restraints weight = 49771.561| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 0.55 r_work: 0.3431 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 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 = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 20245 Z= 0.193 Angle : 0.691 13.209 27537 Z= 0.370 Chirality : 0.047 0.196 3036 Planarity : 0.004 0.036 3496 Dihedral : 9.517 72.089 3304 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.79 % Allowed : 8.22 % 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 are not related in a simple way. whole: -0.71 (0.16), residues: 2460 helix: -1.80 (0.62), residues: 24 sheet: -0.88 (0.15), residues: 895 loop : -0.07 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 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/Z covalent geometry : bond 0.00382 / 0.19 (20181) covalent geometry : angle 0.65950 / 0.36 (27393) SS BOND : bond 0.01585 / 1.08 ( 48) SS BOND : angle 3.23917 / 2.42 ( 96) hydrogen bonds : bond 0.05618 / 3.65 ( 688) hydrogen bonds : angle 7.00373 / 4.83 ( 1908) link_ALPHA1-3 : bond 0.00523 / 0.33 ( 4) link_ALPHA1-3 : angle 2.25931 / 1.20 ( 12) link_ALPHA1-6 : bond 0.00512 / 0.32 ( 4) link_ALPHA1-6 : angle 1.45058 / 0.84 ( 12) link_BETA1-4 : bond 0.00779 / 0.52 ( 8) link_BETA1-4 : angle 2.34891 / 1.49 ( 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 326 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 309 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8055 (m-40) cc_final: 0.7764 (m-40) REVERT: B 50 GLN cc_start: 0.8613 (pt0) cc_final: 0.8290 (pt0) REVERT: F 84 ASN cc_start: 0.8137 (m-40) cc_final: 0.7838 (m-40) REVERT: G 50 GLN cc_start: 0.8627 (pt0) cc_final: 0.8299 (pt0) REVERT: I 84 ASN cc_start: 0.8047 (m-40) cc_final: 0.7662 (m-40) REVERT: J 50 GLN cc_start: 0.8626 (pt0) cc_final: 0.8307 (pt0) REVERT: L 84 ASN cc_start: 0.8090 (m-40) cc_final: 0.7788 (m-40) REVERT: M 50 GLN cc_start: 0.8605 (pt0) cc_final: 0.8280 (pt0) REVERT: N 165 MET cc_start: 0.8795 (mtp) cc_final: 0.8401 (ttm) REVERT: N 312 SER cc_start: 0.8382 (t) cc_final: 0.8123 (p) outliers start: 17 outliers final: 12 residues processed: 321 average time/residue: 1.2913 time to fit residues: 472.3471 Evaluate side-chains 317 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 305 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 209 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 143 optimal weight: 0.1980 chunk 235 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 113 ASN I 82 GLN J 98 GLN L 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.175602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.155028 restraints weight = 54167.227| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 0.64 r_work: 0.3431 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 20245 Z= 0.152 Angle : 0.640 11.286 27537 Z= 0.342 Chirality : 0.046 0.173 3036 Planarity : 0.004 0.035 3496 Dihedral : 8.884 65.723 3304 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 0.65 % Allowed : 8.36 % 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 are not related in a simple way. whole: -0.67 (0.16), residues: 2460 helix: -1.63 (0.65), residues: 24 sheet: -0.84 (0.15), residues: 895 loop : -0.06 (0.17), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 9 TYR 0.018 0.002 TYR K 45 PHE 0.014 0.001 PHE N 334 TRP 0.015 0.001 TRP K 102 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (20181) covalent geometry : angle 0.61373 / 0.33 (27393) SS BOND : bond 0.01212 / 0.83 ( 48) SS BOND : angle 2.79822 / 2.12 ( 96) hydrogen bonds : bond 0.04951 / 3.21 ( 688) hydrogen bonds : angle 6.79367 / 4.68 ( 1908) link_ALPHA1-3 : bond 0.00741 / 0.46 ( 4) link_ALPHA1-3 : angle 2.19425 / 1.15 ( 12) link_ALPHA1-6 : bond 0.00592 / 0.37 ( 4) link_ALPHA1-6 : angle 1.40094 / 0.81 ( 12) link_BETA1-4 : bond 0.00592 / 0.40 ( 8) link_BETA1-4 : angle 2.28234 / 1.44 ( 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: 14 poor density : 315 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8054 (m-40) cc_final: 0.7752 (m-40) REVERT: F 84 ASN cc_start: 0.8093 (m-40) cc_final: 0.7785 (m-40) REVERT: H 165 MET cc_start: 0.8710 (mtp) cc_final: 0.8164 (ttm) REVERT: I 84 ASN cc_start: 0.8033 (m-40) cc_final: 0.7702 (m-40) REVERT: K 165 MET cc_start: 0.8703 (mtp) cc_final: 0.8156 (ttm) REVERT: L 84 ASN cc_start: 0.8087 (m-40) cc_final: 0.7761 (m-40) REVERT: N 165 MET cc_start: 0.8704 (mtp) cc_final: 0.8160 (ttm) REVERT: N 312 SER cc_start: 0.8333 (t) cc_final: 0.8085 (p) outliers start: 14 outliers final: 11 residues processed: 325 average time/residue: 1.2788 time to fit residues: 474.0049 Evaluate side-chains 311 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 300 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 45 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN F 39 GLN G 98 GLN I 39 GLN J 98 GLN L 39 GLN M 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.169154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.149572 restraints weight = 47593.868| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 0.53 r_work: 0.3388 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work: 0.3153 rms_B_bonded: 4.28 restraints_weight: 0.1250 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 20245 Z= 0.325 Angle : 0.851 14.700 27537 Z= 0.455 Chirality : 0.050 0.230 3036 Planarity : 0.005 0.042 3496 Dihedral : 10.515 82.425 3303 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.51 % Allowed : 8.78 % Favored : 90.71 % 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 are not related in a simple way. whole: -0.69 (0.16), residues: 2460 helix: -2.21 (0.44), residues: 24 sheet: -0.75 (0.15), residues: 921 loop : -0.12 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 80 TYR 0.021 0.004 TYR N 45 PHE 0.014 0.003 PHE N 334 TRP 0.020 0.003 TRP D 102 HIS 0.010 0.002 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.32 (20181) covalent geometry : angle 0.80953 / 0.44 (27393) SS BOND : bond 0.02716 / 1.86 ( 48) SS BOND : angle 4.25084 / 3.31 ( 96) hydrogen bonds : bond 0.07004 / 4.55 ( 688) hydrogen bonds : angle 7.29579 / 5.03 ( 1908) link_ALPHA1-3 : bond 0.00212 / 0.13 ( 4) link_ALPHA1-3 : angle 2.58307 / 1.44 ( 12) link_ALPHA1-6 : bond 0.00470 / 0.29 ( 4) link_ALPHA1-6 : angle 1.53426 / 0.87 ( 12) link_BETA1-4 : bond 0.01253 / 0.83 ( 8) link_BETA1-4 : angle 2.52055 / 1.60 ( 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 323 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 312 time to evaluate : 1.147 Fit side-chains REVERT: I 34 MET cc_start: 0.8971 (mmm) cc_final: 0.8645 (mmm) REVERT: I 84 ASN cc_start: 0.8137 (m-40) cc_final: 0.7769 (m-40) REVERT: L 34 MET cc_start: 0.8985 (mmm) cc_final: 0.8674 (mmm) REVERT: N 312 SER cc_start: 0.8460 (t) cc_final: 0.8159 (p) outliers start: 11 outliers final: 10 residues processed: 322 average time/residue: 1.3158 time to fit residues: 482.6512 Evaluate side-chains 321 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 311 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 chunk 188 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN F 84 ASN G 27 GLN G 98 GLN J 98 GLN L 84 ASN L 113 ASN M 27 GLN M 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.167641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.148154 restraints weight = 47292.871| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 0.54 r_work: 0.3394 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 20245 Z= 0.280 Angle : 0.801 11.393 27537 Z= 0.430 Chirality : 0.049 0.207 3036 Planarity : 0.005 0.042 3496 Dihedral : 10.243 78.471 3303 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.51 % Allowed : 9.25 % 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 are not related in a simple way. whole: -0.72 (0.16), residues: 2460 helix: -2.20 (0.50), residues: 24 sheet: -0.75 (0.15), residues: 913 loop : -0.16 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 251 TYR 0.021 0.003 TYR N 45 PHE 0.013 0.002 PHE N 334 TRP 0.019 0.002 TRP K 102 HIS 0.008 0.002 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.27 (20181) covalent geometry : angle 0.76664 / 0.42 (27393) SS BOND : bond 0.02274 / 1.55 ( 48) SS BOND : angle 3.71622 / 2.89 ( 96) hydrogen bonds : bond 0.06671 / 4.33 ( 688) hydrogen bonds : angle 7.26234 / 5.01 ( 1908) link_ALPHA1-3 : bond 0.00022 / 0.01 ( 4) link_ALPHA1-3 : angle 2.63235 / 1.43 ( 12) link_ALPHA1-6 : bond 0.00448 / 0.28 ( 4) link_ALPHA1-6 : angle 1.49263 / 0.86 ( 12) link_BETA1-4 : bond 0.01079 / 0.71 ( 8) link_BETA1-4 : angle 2.38643 / 1.52 ( 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 322 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 311 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7984 (m-40) cc_final: 0.7657 (m-40) REVERT: F 84 ASN cc_start: 0.8008 (m-40) cc_final: 0.7681 (m-40) REVERT: H 165 MET cc_start: 0.8790 (mtp) cc_final: 0.8273 (ttm) REVERT: I 34 MET cc_start: 0.8910 (mmm) cc_final: 0.8570 (mmm) REVERT: I 84 ASN cc_start: 0.8048 (m-40) cc_final: 0.7693 (m-40) REVERT: K 165 MET cc_start: 0.8781 (mtp) cc_final: 0.8266 (ttm) REVERT: L 34 MET cc_start: 0.8931 (mmm) cc_final: 0.8601 (mmm) REVERT: L 84 ASN cc_start: 0.8000 (m-40) cc_final: 0.7677 (m-40) REVERT: N 165 MET cc_start: 0.8785 (mtp) cc_final: 0.8272 (ttm) REVERT: N 312 SER cc_start: 0.8433 (t) cc_final: 0.8143 (p) outliers start: 11 outliers final: 9 residues processed: 321 average time/residue: 1.3781 time to fit residues: 502.9988 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 : 1.066 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 79 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN F 39 GLN F 113 ASN I 39 GLN J 98 GLN L 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.174481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.154266 restraints weight = 48026.692| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 0.58 r_work: 0.3440 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 20245 Z= 0.163 Angle : 0.658 8.250 27537 Z= 0.352 Chirality : 0.047 0.165 3036 Planarity : 0.004 0.035 3496 Dihedral : 9.137 67.546 3303 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.51 % Allowed : 9.34 % Favored : 90.15 % 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 are not related in a simple way. whole: -0.66 (0.16), residues: 2460 helix: -1.66 (0.66), residues: 24 sheet: -0.83 (0.15), residues: 895 loop : -0.05 (0.17), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 9 TYR 0.019 0.002 TYR N 45 PHE 0.015 0.001 PHE H 334 TRP 0.016 0.002 TRP H 102 HIS 0.003 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (20181) covalent geometry : angle 0.63454 / 0.34 (27393) SS BOND : bond 0.01302 / 0.89 ( 48) SS BOND : angle 2.65308 / 2.06 ( 96) hydrogen bonds : bond 0.05179 / 3.36 ( 688) hydrogen bonds : angle 6.83876 / 4.71 ( 1908) link_ALPHA1-3 : bond 0.00737 / 0.44 ( 4) link_ALPHA1-3 : angle 2.18516 / 1.15 ( 12) link_ALPHA1-6 : bond 0.00611 / 0.38 ( 4) link_ALPHA1-6 : angle 1.40222 / 0.80 ( 12) link_BETA1-4 : bond 0.00631 / 0.43 ( 8) link_BETA1-4 : angle 2.30984 / 1.47 ( 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 309 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 298 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.7991 (m-40) cc_final: 0.7669 (m-40) REVERT: F 84 ASN cc_start: 0.8063 (m-40) cc_final: 0.7746 (m-40) REVERT: H 165 MET cc_start: 0.8729 (mtp) cc_final: 0.8327 (ttm) REVERT: I 84 ASN cc_start: 0.7990 (m-40) cc_final: 0.7628 (m-40) REVERT: K 165 MET cc_start: 0.8735 (mtp) cc_final: 0.8330 (ttm) REVERT: L 84 ASN cc_start: 0.8045 (m-40) cc_final: 0.7732 (m-40) REVERT: N 165 MET cc_start: 0.8726 (mtp) cc_final: 0.8321 (ttm) REVERT: N 312 SER cc_start: 0.8401 (t) cc_final: 0.8140 (p) outliers start: 11 outliers final: 10 residues processed: 308 average time/residue: 1.4243 time to fit residues: 499.7982 Evaluate side-chains 304 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 294 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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 65 LYS 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: 4.9990 chunk 23 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 208 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN B 98 GLN F 39 GLN G 98 GLN I 39 GLN J 98 GLN L 39 GLN M 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.172089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.152421 restraints weight = 45261.808| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 0.52 r_work: 0.3435 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work: 0.3181 rms_B_bonded: 4.67 restraints_weight: 0.1250 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 20245 Z= 0.212 Angle : 0.714 9.799 27537 Z= 0.381 Chirality : 0.047 0.182 3036 Planarity : 0.004 0.036 3496 Dihedral : 9.576 72.509 3303 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.46 % Allowed : 9.53 % 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 are not related in a simple way. whole: -0.69 (0.16), residues: 2460 helix: -1.92 (0.55), residues: 24 sheet: -0.83 (0.15), residues: 895 loop : -0.08 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 251 TYR 0.019 0.002 TYR N 45 PHE 0.013 0.002 PHE N 334 TRP 0.018 0.002 TRP K 102 HIS 0.006 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (20181) covalent geometry : angle 0.68572 / 0.37 (27393) SS BOND : bond 0.01743 / 1.19 ( 48) SS BOND : angle 3.09127 / 2.42 ( 96) hydrogen bonds : bond 0.05779 / 3.75 ( 688) hydrogen bonds : angle 6.96513 / 4.80 ( 1908) link_ALPHA1-3 : bond 0.00395 / 0.25 ( 4) link_ALPHA1-3 : angle 2.40761 / 1.28 ( 12) link_ALPHA1-6 : bond 0.00479 / 0.30 ( 4) link_ALPHA1-6 : angle 1.45362 / 0.84 ( 12) link_BETA1-4 : bond 0.00874 / 0.58 ( 8) link_BETA1-4 : angle 2.36686 / 1.49 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18581.13 seconds wall clock time: 315 minutes 8.95 seconds (18908.95 seconds total)