Starting phenix.real_space_refine on Fri Mar 6 19:33:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nx0_49897/03_2026/9nx0_49897_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nx0_49897/03_2026/9nx0_49897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nx0_49897/03_2026/9nx0_49897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nx0_49897/03_2026/9nx0_49897.map" model { file = "/net/cci-nas-00/data/ceres_data/9nx0_49897/03_2026/9nx0_49897_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nx0_49897/03_2026/9nx0_49897_trim.cif" } resolution = 3.06 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= 0.007 sd= 0.055 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 P 5 5.49 5 S 130 5.16 5 C 10940 2.51 5 N 2700 2.21 5 O 3055 1.98 5 H 15740 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32570 Number of models: 1 Model: "" Number of chains: 30 Chain: "G" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 90 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 90 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 90 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 90 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 90 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6318 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6377 Chain: "B" Number of atoms: 6318 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6377 Chain: "E" Number of atoms: 6318 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6377 Chain: "D" Number of atoms: 6318 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6377 Chain: "C" Number of atoms: 6318 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 392, 6304 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6377 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 10.95, per 1000 atoms: 0.34 Number of scatterers: 32570 At special positions: 0 Unit cell: (101.426, 98.189, 166.166, 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) S 130 16.00 P 5 15.00 O 3055 8.00 N 2700 7.00 C 10940 6.00 H 15740 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 8 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 12 " distance=2.01 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 8 " distance=2.03 Simple disulfide: pdb=" SG CYS H 3 " - pdb=" SG CYS H 12 " distance=2.01 Simple disulfide: pdb=" SG CYS I 2 " - pdb=" SG CYS I 8 " distance=2.03 Simple disulfide: pdb=" SG CYS I 3 " - pdb=" SG CYS I 12 " distance=2.01 Simple disulfide: pdb=" SG CYS J 2 " - pdb=" SG CYS J 8 " distance=2.03 Simple disulfide: pdb=" SG CYS J 3 " - pdb=" SG CYS J 12 " distance=2.01 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 8 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 12 " distance=2.01 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " 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=5, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG B 501 " - " ASN B 67 " " NAG C 501 " - " ASN C 67 " " NAG D 501 " - " ASN D 67 " " NAG E 501 " - " ASN E 67 " " NAG K 1 " - " ASN A 23 " " NAG L 1 " - " ASN A 110 " " NAG M 1 " - " ASN B 23 " " NAG N 1 " - " ASN B 110 " " NAG O 1 " - " ASN E 23 " " NAG P 1 " - " ASN E 110 " " NAG Q 1 " - " ASN D 23 " " NAG R 1 " - " ASN D 110 " " NAG S 1 " - " ASN C 23 " " NAG T 1 " - " ASN C 110 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 46.5% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'G' and resid 1 through 5 Processing helix chain 'G' and resid 8 through 12 Processing helix chain 'H' and resid 1 through 5 Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'I' and resid 1 through 5 Processing helix chain 'I' and resid 8 through 12 Processing helix chain 'J' and resid 1 through 5 Processing helix chain 'J' and resid 8 through 12 Processing helix chain 'F' and resid 1 through 5 Processing helix chain 'F' and resid 8 through 12 Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.567A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.582A pdb=" N GLN A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.534A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.719A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 320 removed outlier: 3.639A pdb=" N ALA A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 466 removed outlier: 3.697A pdb=" N TRP A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.567A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.581A pdb=" N GLN B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 228 removed outlier: 3.535A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.721A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.639A pdb=" N ALA B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 466 removed outlier: 3.697A pdb=" N TRP B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.567A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.581A pdb=" N GLN E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE E 84 " --> pdb=" O ASP E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 84' Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 228 removed outlier: 3.534A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.719A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 320 removed outlier: 3.638A pdb=" N ALA E 317 " --> pdb=" O LEU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 466 removed outlier: 3.698A pdb=" N TRP E 437 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 478 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.568A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.582A pdb=" N GLN D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE D 84 " --> pdb=" O ASP D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 84' Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 228 removed outlier: 3.535A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.720A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 320 removed outlier: 3.639A pdb=" N ALA D 317 " --> pdb=" O LEU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 466 removed outlier: 3.698A pdb=" N TRP D 437 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.568A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.581A pdb=" N GLN C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 228 removed outlier: 3.534A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.719A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.639A pdb=" N ALA C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 466 removed outlier: 3.697A pdb=" N TRP C 437 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 7.166A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU A 28 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 10.676A pdb=" N MET A 159 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N VAL A 30 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU A 161 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE A 32 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ASP A 163 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 34 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.072A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.072A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 185 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.165A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU B 28 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N MET B 159 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N VAL B 30 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N GLU B 161 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE B 32 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N ASP B 163 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 34 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.073A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.073A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 185 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AB1, first strand: chain 'E' and resid 77 through 79 removed outlier: 7.165A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR E 29 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU E 28 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N MET E 159 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N VAL E 30 " --> pdb=" O MET E 159 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N GLU E 161 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE E 32 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N ASP E 163 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU E 34 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 89 through 91 removed outlier: 5.073A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 89 through 91 removed outlier: 5.073A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 185 " --> pdb=" O TYR E 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 79 removed outlier: 7.165A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR D 29 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU D 28 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N MET D 159 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N VAL D 30 " --> pdb=" O MET D 159 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU D 161 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE D 32 " --> pdb=" O GLU D 161 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ASP D 163 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 34 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 5.071A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 5.071A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB9, first strand: chain 'C' and resid 77 through 79 removed outlier: 7.165A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N LEU C 28 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N MET C 159 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N VAL C 30 " --> pdb=" O MET C 159 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N GLU C 161 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 32 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N ASP C 163 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU C 34 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 89 through 91 removed outlier: 5.073A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 89 through 91 removed outlier: 5.073A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 185 " --> pdb=" O TYR C 194 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.94 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15700 1.03 - 1.23: 96 1.23 - 1.43: 7244 1.43 - 1.62: 9795 1.62 - 1.82: 190 Bond restraints: 33025 Sorted by residual: bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 33020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 57932 1.74 - 3.47: 1157 3.47 - 5.21: 161 5.21 - 6.94: 30 6.94 - 8.68: 10 Bond angle restraints: 59290 Sorted by residual: angle pdb=" CA ARG H 11 " pdb=" CB ARG H 11 " pdb=" CG ARG H 11 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CA ARG G 11 " pdb=" CB ARG G 11 " pdb=" CG ARG G 11 " ideal model delta sigma weight residual 114.10 120.41 -6.31 2.00e+00 2.50e-01 9.97e+00 angle pdb=" CA ARG F 11 " pdb=" CB ARG F 11 " pdb=" CG ARG F 11 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.84e+00 angle pdb=" CA ARG I 11 " pdb=" CB ARG I 11 " pdb=" CG ARG I 11 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.82e+00 angle pdb=" CA ARG J 11 " pdb=" CB ARG J 11 " pdb=" CG ARG J 11 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.76e+00 ... (remaining 59285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 14316 16.16 - 32.31: 1329 32.31 - 48.47: 360 48.47 - 64.63: 130 64.63 - 80.78: 35 Dihedral angle restraints: 16170 sinusoidal: 8865 harmonic: 7305 Sorted by residual: dihedral pdb=" CB CYS H 3 " pdb=" SG CYS H 3 " pdb=" SG CYS H 12 " pdb=" CB CYS H 12 " ideal model delta sinusoidal sigma weight residual -86.00 -5.22 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS G 3 " pdb=" SG CYS G 3 " pdb=" SG CYS G 12 " pdb=" CB CYS G 12 " ideal model delta sinusoidal sigma weight residual -86.00 -5.25 -80.75 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS I 3 " pdb=" SG CYS I 3 " pdb=" SG CYS I 12 " pdb=" CB CYS I 12 " ideal model delta sinusoidal sigma weight residual -86.00 -5.27 -80.73 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 16167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1504 0.026 - 0.053: 704 0.053 - 0.079: 273 0.079 - 0.105: 111 0.105 - 0.132: 88 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CA ILE D 168 " pdb=" N ILE D 168 " pdb=" C ILE D 168 " pdb=" CB ILE D 168 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE D 122 " pdb=" N ILE D 122 " pdb=" C ILE D 122 " pdb=" CB ILE D 122 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE A 168 " pdb=" N ILE A 168 " pdb=" C ILE A 168 " pdb=" CB ILE A 168 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 2677 not shown) Planarity restraints: 4755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB AHIS A 114 " -0.005 2.00e-02 2.50e+03 3.33e-02 2.49e+01 pdb=" CG AHIS A 114 " -0.071 2.00e-02 2.50e+03 pdb=" ND1AHIS A 114 " 0.007 2.00e-02 2.50e+03 pdb=" CD2AHIS A 114 " -0.002 2.00e-02 2.50e+03 pdb=" CE1AHIS A 114 " -0.009 2.00e-02 2.50e+03 pdb=" NE2AHIS A 114 " -0.008 2.00e-02 2.50e+03 pdb=" HD1AHIS A 114 " 0.049 2.00e-02 2.50e+03 pdb=" HD2AHIS A 114 " 0.047 2.00e-02 2.50e+03 pdb=" HE1AHIS A 114 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 100 " -0.018 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" CG ASP C 100 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASP C 100 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP C 100 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 100 " 0.018 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" CG ASP B 100 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASP B 100 " 0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP B 100 " 0.024 2.00e-02 2.50e+03 ... (remaining 4752 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1482 2.19 - 2.79: 63833 2.79 - 3.40: 87020 3.40 - 4.00: 118172 4.00 - 4.60: 180718 Nonbonded interactions: 451225 Sorted by model distance: nonbonded pdb=" O CYS D 316 " pdb=" H ARG D 321 " model vdw 1.589 2.450 nonbonded pdb=" O CYS A 316 " pdb=" H ARG A 321 " model vdw 1.589 2.450 nonbonded pdb=" O CYS E 316 " pdb=" H ARG E 321 " model vdw 1.589 2.450 nonbonded pdb=" O CYS B 316 " pdb=" H ARG B 321 " model vdw 1.589 2.450 nonbonded pdb=" O CYS C 316 " pdb=" H ARG C 321 " model vdw 1.589 2.450 ... (remaining 451220 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 502)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 502)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 502)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 502)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 502)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.50 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.930 Find NCS groups from input model: 0.880 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: 0.000 Load rotamer database and sin/cos tables:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 0.060 17335 Z= 0.204 Angle : 0.947 49.471 23650 Z= 0.456 Chirality : 0.041 0.132 2680 Planarity : 0.005 0.038 2890 Dihedral : 14.552 79.224 6680 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.55 % Allowed : 8.41 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 0.56 (0.18), residues: 1995 helix: 1.74 (0.16), residues: 870 sheet: -0.45 (0.24), residues: 440 loop : -0.78 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 132 TYR 0.010 0.002 TYR C 117 PHE 0.013 0.001 PHE B 32 TRP 0.026 0.002 TRP E 315 HIS 0.005 0.001 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00386 (17285) covalent geometry : angle 0.60650 (23535) SS BOND : bond 0.00999 ( 20) SS BOND : angle 17.54653 ( 40) hydrogen bonds : bond 0.10803 ( 890) hydrogen bonds : angle 5.22044 ( 2835) Misc. bond : bond 0.05991 ( 5) link_BETA1-4 : bond 0.00263 ( 10) link_BETA1-4 : angle 1.28203 ( 30) link_NAG-ASN : bond 0.00130 ( 15) link_NAG-ASN : angle 1.95982 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8656 (mm) outliers start: 10 outliers final: 4 residues processed: 170 average time/residue: 0.2296 time to fit residues: 63.0062 Evaluate side-chains 132 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073430 restraints weight = 139662.962| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.11 r_work: 0.2881 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17335 Z= 0.121 Angle : 0.530 6.265 23650 Z= 0.270 Chirality : 0.039 0.146 2680 Planarity : 0.004 0.064 2890 Dihedral : 8.513 59.523 2860 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.77 % Allowed : 8.90 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 0.90 (0.19), residues: 1995 helix: 2.08 (0.16), residues: 870 sheet: -0.16 (0.24), residues: 450 loop : -0.80 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 11 TYR 0.008 0.001 TYR D 273 PHE 0.006 0.001 PHE C 455 TRP 0.010 0.001 TRP F 10 HIS 0.001 0.000 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00261 (17285) covalent geometry : angle 0.52305 (23535) SS BOND : bond 0.00409 ( 20) SS BOND : angle 0.87858 ( 40) hydrogen bonds : bond 0.04868 ( 890) hydrogen bonds : angle 4.42627 ( 2835) Misc. bond : bond 0.00159 ( 5) link_BETA1-4 : bond 0.00272 ( 10) link_BETA1-4 : angle 1.00050 ( 30) link_NAG-ASN : bond 0.00077 ( 15) link_NAG-ASN : angle 1.80492 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8729 (mm) REVERT: C 227 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8644 (mp) REVERT: C 445 ASP cc_start: 0.7715 (t0) cc_final: 0.7466 (t0) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.2461 time to fit residues: 57.1437 Evaluate side-chains 139 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 315 TRP Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 315 TRP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 259 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 31 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.066796 restraints weight = 140773.515| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.13 r_work: 0.2741 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17335 Z= 0.209 Angle : 0.585 6.941 23650 Z= 0.301 Chirality : 0.041 0.160 2680 Planarity : 0.004 0.049 2890 Dihedral : 8.339 63.376 2860 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.10 % Allowed : 8.35 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 0.85 (0.18), residues: 1995 helix: 2.18 (0.16), residues: 840 sheet: -0.34 (0.24), residues: 440 loop : -0.77 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 11 TYR 0.019 0.002 TYR E 194 PHE 0.037 0.002 PHE D 455 TRP 0.011 0.001 TRP C 315 HIS 0.002 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00487 (17285) covalent geometry : angle 0.57745 (23535) SS BOND : bond 0.00386 ( 20) SS BOND : angle 1.00935 ( 40) hydrogen bonds : bond 0.04754 ( 890) hydrogen bonds : angle 4.31060 ( 2835) Misc. bond : bond 0.00145 ( 5) link_BETA1-4 : bond 0.00112 ( 10) link_BETA1-4 : angle 1.08110 ( 30) link_NAG-ASN : bond 0.00360 ( 15) link_NAG-ASN : angle 1.99407 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.9018 (p0) cc_final: 0.8752 (p0) REVERT: A 294 TYR cc_start: 0.8689 (m-80) cc_final: 0.8437 (m-80) REVERT: B 212 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8730 (mm) REVERT: B 294 TYR cc_start: 0.8460 (m-80) cc_final: 0.8059 (m-80) REVERT: B 445 ASP cc_start: 0.7758 (t0) cc_final: 0.7386 (t0) REVERT: D 450 MET cc_start: 0.7659 (ttm) cc_final: 0.7444 (mmt) REVERT: C 445 ASP cc_start: 0.7774 (t0) cc_final: 0.7514 (t0) outliers start: 20 outliers final: 12 residues processed: 148 average time/residue: 0.2555 time to fit residues: 59.4167 Evaluate side-chains 136 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 431 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.067065 restraints weight = 126813.974| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.01 r_work: 0.2748 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17335 Z= 0.158 Angle : 0.526 5.896 23650 Z= 0.268 Chirality : 0.040 0.141 2680 Planarity : 0.004 0.048 2890 Dihedral : 8.038 63.069 2860 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.82 % Allowed : 8.74 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 1.02 (0.18), residues: 1995 helix: 2.31 (0.16), residues: 840 sheet: -0.25 (0.24), residues: 450 loop : -0.66 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 11 TYR 0.014 0.001 TYR A 194 PHE 0.011 0.001 PHE C 319 TRP 0.010 0.001 TRP D 59 HIS 0.002 0.001 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00365 (17285) covalent geometry : angle 0.51905 (23535) SS BOND : bond 0.00357 ( 20) SS BOND : angle 0.82101 ( 40) hydrogen bonds : bond 0.04466 ( 890) hydrogen bonds : angle 4.18641 ( 2835) Misc. bond : bond 0.00013 ( 5) link_BETA1-4 : bond 0.00135 ( 10) link_BETA1-4 : angle 1.15108 ( 30) link_NAG-ASN : bond 0.00122 ( 15) link_NAG-ASN : angle 1.79038 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 TYR cc_start: 0.8687 (m-80) cc_final: 0.8442 (m-80) REVERT: B 212 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8703 (mm) REVERT: B 294 TYR cc_start: 0.8437 (m-80) cc_final: 0.8106 (m-80) REVERT: B 445 ASP cc_start: 0.7661 (t0) cc_final: 0.7296 (t0) REVERT: E 258 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8640 (tm-30) outliers start: 15 outliers final: 11 residues processed: 140 average time/residue: 0.2560 time to fit residues: 56.6059 Evaluate side-chains 133 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 431 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.066392 restraints weight = 131617.878| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.06 r_work: 0.2728 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17335 Z= 0.173 Angle : 0.521 5.349 23650 Z= 0.267 Chirality : 0.040 0.137 2680 Planarity : 0.004 0.033 2890 Dihedral : 7.835 60.532 2860 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.71 % Allowed : 9.29 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 1.09 (0.18), residues: 1995 helix: 2.37 (0.16), residues: 840 sheet: -0.21 (0.24), residues: 450 loop : -0.64 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 11 TYR 0.017 0.001 TYR E 273 PHE 0.017 0.001 PHE D 455 TRP 0.007 0.001 TRP C 315 HIS 0.004 0.001 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00405 (17285) covalent geometry : angle 0.51417 (23535) SS BOND : bond 0.00409 ( 20) SS BOND : angle 0.84016 ( 40) hydrogen bonds : bond 0.04367 ( 890) hydrogen bonds : angle 4.13791 ( 2835) Misc. bond : bond 0.00014 ( 5) link_BETA1-4 : bond 0.00079 ( 10) link_BETA1-4 : angle 1.10657 ( 30) link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 1.76620 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 11 ARG cc_start: 0.7692 (ttt-90) cc_final: 0.7453 (ptm160) REVERT: B 212 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8691 (mm) REVERT: B 294 TYR cc_start: 0.8458 (m-80) cc_final: 0.8165 (m-80) REVERT: B 445 ASP cc_start: 0.7853 (t0) cc_final: 0.7498 (t0) REVERT: E 258 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8626 (tm-30) outliers start: 13 outliers final: 10 residues processed: 138 average time/residue: 0.2607 time to fit residues: 56.6738 Evaluate side-chains 134 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 431 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 44 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.065529 restraints weight = 122224.210| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.96 r_work: 0.2714 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17335 Z= 0.205 Angle : 0.535 6.313 23650 Z= 0.274 Chirality : 0.040 0.140 2680 Planarity : 0.004 0.031 2890 Dihedral : 7.579 58.965 2856 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.88 % Allowed : 9.51 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 1.12 (0.18), residues: 1995 helix: 2.41 (0.16), residues: 840 sheet: -0.20 (0.25), residues: 450 loop : -0.64 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 11 TYR 0.014 0.001 TYR A 194 PHE 0.014 0.001 PHE C 99 TRP 0.008 0.001 TRP B 437 HIS 0.005 0.001 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00481 (17285) covalent geometry : angle 0.52732 (23535) SS BOND : bond 0.00427 ( 20) SS BOND : angle 0.81923 ( 40) hydrogen bonds : bond 0.04400 ( 890) hydrogen bonds : angle 4.16408 ( 2835) Misc. bond : bond 0.00015 ( 5) link_BETA1-4 : bond 0.00058 ( 10) link_BETA1-4 : angle 1.13215 ( 30) link_NAG-ASN : bond 0.00259 ( 15) link_NAG-ASN : angle 1.83052 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8683 (mm) REVERT: B 294 TYR cc_start: 0.8614 (m-80) cc_final: 0.8342 (m-80) REVERT: B 445 ASP cc_start: 0.7862 (t0) cc_final: 0.7588 (t0) REVERT: E 258 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8608 (tm-30) outliers start: 16 outliers final: 15 residues processed: 137 average time/residue: 0.2521 time to fit residues: 54.3638 Evaluate side-chains 136 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 182 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.066754 restraints weight = 145256.591| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.20 r_work: 0.2733 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17335 Z= 0.107 Angle : 0.489 6.626 23650 Z= 0.248 Chirality : 0.039 0.138 2680 Planarity : 0.003 0.034 2890 Dihedral : 7.263 58.933 2856 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.82 % Allowed : 9.78 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 1.27 (0.18), residues: 1995 helix: 2.54 (0.16), residues: 840 sheet: -0.15 (0.25), residues: 450 loop : -0.54 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 11 TYR 0.011 0.001 TYR B 194 PHE 0.010 0.001 PHE B 319 TRP 0.007 0.001 TRP E 59 HIS 0.004 0.001 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00235 (17285) covalent geometry : angle 0.48248 (23535) SS BOND : bond 0.00389 ( 20) SS BOND : angle 0.81143 ( 40) hydrogen bonds : bond 0.04175 ( 890) hydrogen bonds : angle 4.00294 ( 2835) Misc. bond : bond 0.00012 ( 5) link_BETA1-4 : bond 0.00173 ( 10) link_BETA1-4 : angle 1.14972 ( 30) link_NAG-ASN : bond 0.00075 ( 15) link_NAG-ASN : angle 1.62299 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8640 (mm) REVERT: B 294 TYR cc_start: 0.8607 (m-80) cc_final: 0.8361 (m-80) REVERT: B 445 ASP cc_start: 0.7857 (t0) cc_final: 0.7613 (t0) REVERT: E 258 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8586 (tm-30) outliers start: 15 outliers final: 12 residues processed: 138 average time/residue: 0.2593 time to fit residues: 56.3277 Evaluate side-chains 135 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.066892 restraints weight = 136566.806| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.12 r_work: 0.2732 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17335 Z= 0.135 Angle : 0.487 6.344 23650 Z= 0.248 Chirality : 0.039 0.138 2680 Planarity : 0.003 0.032 2890 Dihedral : 7.019 58.969 2856 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.66 % Allowed : 9.89 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 1.37 (0.19), residues: 1995 helix: 2.60 (0.16), residues: 840 sheet: -0.09 (0.25), residues: 450 loop : -0.47 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 11 TYR 0.014 0.001 TYR E 273 PHE 0.015 0.001 PHE C 455 TRP 0.008 0.001 TRP B 437 HIS 0.004 0.000 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00314 (17285) covalent geometry : angle 0.47970 (23535) SS BOND : bond 0.00415 ( 20) SS BOND : angle 0.82859 ( 40) hydrogen bonds : bond 0.04055 ( 890) hydrogen bonds : angle 3.96624 ( 2835) Misc. bond : bond 0.00020 ( 5) link_BETA1-4 : bond 0.00102 ( 10) link_BETA1-4 : angle 1.12103 ( 30) link_NAG-ASN : bond 0.00111 ( 15) link_NAG-ASN : angle 1.68001 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8663 (mm) REVERT: B 294 TYR cc_start: 0.8669 (m-80) cc_final: 0.8454 (m-80) REVERT: E 258 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8606 (tm-30) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 0.2575 time to fit residues: 55.5455 Evaluate side-chains 132 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 18 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 93 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.067916 restraints weight = 130048.105| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.05 r_work: 0.2759 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17335 Z= 0.099 Angle : 0.471 6.604 23650 Z= 0.237 Chirality : 0.038 0.136 2680 Planarity : 0.003 0.033 2890 Dihedral : 6.905 59.676 2856 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.66 % Allowed : 9.89 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 1.34 (0.19), residues: 1995 helix: 2.48 (0.16), residues: 870 sheet: -0.04 (0.25), residues: 450 loop : -0.55 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 11 TYR 0.010 0.001 TYR E 273 PHE 0.018 0.001 PHE D 455 TRP 0.007 0.001 TRP E 59 HIS 0.004 0.000 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00223 (17285) covalent geometry : angle 0.46404 (23535) SS BOND : bond 0.00402 ( 20) SS BOND : angle 0.82309 ( 40) hydrogen bonds : bond 0.03904 ( 890) hydrogen bonds : angle 3.86872 ( 2835) Misc. bond : bond 0.00006 ( 5) link_BETA1-4 : bond 0.00224 ( 10) link_BETA1-4 : angle 1.09775 ( 30) link_NAG-ASN : bond 0.00099 ( 15) link_NAG-ASN : angle 1.55637 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8664 (mm) REVERT: E 258 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8620 (tm-30) outliers start: 12 outliers final: 11 residues processed: 131 average time/residue: 0.2504 time to fit residues: 51.8131 Evaluate side-chains 131 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 94 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 chunk 154 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.068428 restraints weight = 131661.526| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.06 r_work: 0.2772 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17335 Z= 0.098 Angle : 0.462 6.570 23650 Z= 0.233 Chirality : 0.038 0.135 2680 Planarity : 0.003 0.032 2890 Dihedral : 6.799 59.984 2856 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.66 % Allowed : 9.89 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 1.47 (0.19), residues: 1995 helix: 2.59 (0.16), residues: 870 sheet: 0.02 (0.25), residues: 450 loop : -0.48 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 446 TYR 0.011 0.001 TYR E 273 PHE 0.014 0.001 PHE C 455 TRP 0.013 0.001 TRP B 437 HIS 0.004 0.000 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00225 (17285) covalent geometry : angle 0.45547 (23535) SS BOND : bond 0.00414 ( 20) SS BOND : angle 0.81626 ( 40) hydrogen bonds : bond 0.03741 ( 890) hydrogen bonds : angle 3.79231 ( 2835) Misc. bond : bond 0.00004 ( 5) link_BETA1-4 : bond 0.00202 ( 10) link_BETA1-4 : angle 1.09439 ( 30) link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.54009 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8639 (mm) REVERT: E 40 MET cc_start: 0.9483 (mtp) cc_final: 0.9217 (mmm) REVERT: E 258 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8626 (tm-30) outliers start: 12 outliers final: 11 residues processed: 134 average time/residue: 0.2575 time to fit residues: 55.0428 Evaluate side-chains 133 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 172 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 170 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 94 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.068523 restraints weight = 135248.706| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.10 r_work: 0.2772 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17335 Z= 0.097 Angle : 0.461 6.626 23650 Z= 0.232 Chirality : 0.038 0.134 2680 Planarity : 0.003 0.032 2890 Dihedral : 6.764 59.544 2856 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.71 % Allowed : 9.89 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % 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: 1.53 (0.19), residues: 1995 helix: 2.65 (0.16), residues: 870 sheet: 0.05 (0.25), residues: 450 loop : -0.46 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 TYR 0.010 0.001 TYR E 273 PHE 0.014 0.001 PHE C 455 TRP 0.007 0.001 TRP C 315 HIS 0.004 0.000 HIS E 296 Details of bonding type rmsd covalent geometry : bond 0.00221 (17285) covalent geometry : angle 0.45482 (23535) SS BOND : bond 0.00408 ( 20) SS BOND : angle 0.81428 ( 40) hydrogen bonds : bond 0.03685 ( 890) hydrogen bonds : angle 3.75430 ( 2835) Misc. bond : bond 0.00006 ( 5) link_BETA1-4 : bond 0.00216 ( 10) link_BETA1-4 : angle 1.04645 ( 30) link_NAG-ASN : bond 0.00075 ( 15) link_NAG-ASN : angle 1.50399 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8520.16 seconds wall clock time: 144 minutes 46.74 seconds (8686.74 seconds total)