Starting phenix.real_space_refine on Sat Jul 4 15:01:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a5v_11657/07_2026/7a5v_11657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a5v_11657/07_2026/7a5v_11657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7a5v_11657/07_2026/7a5v_11657.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a5v_11657/07_2026/7a5v_11657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a5v_11657/07_2026/7a5v_11657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a5v_11657/07_2026/7a5v_11657.map" model { file = "/net/cci-nas-00/data/ceres_data/7a5v_11657/07_2026/7a5v_11657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a5v_11657/07_2026/7a5v_11657.cif" } resolution = 1.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians S 115 5.16 5 Cl 10 4.86 5 C 13175 2.51 5 N 3190 2.21 5 O 4665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21155 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "O" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 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 chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "Q" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "R" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 105 residue: pdb=" N AMET A 40 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 40 " occ=0.50 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ATYR A 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 66 " occ=0.50 residue: pdb=" N AASN A 85 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 85 " occ=0.50 residue: pdb=" N ASER A 104 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 104 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N AILE A 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 164 " occ=0.50 residue: pdb=" N AVAL A 198 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 198 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N APHE A 212 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 212 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N ATHR A 225 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 225 " occ=0.50 ... (remaining 93 not shown) Time building chain proxies: 6.82, per 1000 atoms: 0.32 Number of scatterers: 21155 At special positions: 0 Unit cell: (142.859, 139.612, 127.437, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 10 17.00 S 115 16.00 O 4665 8.00 N 3190 7.00 C 13175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG ACYS A 136 " - pdb=" SG ACYS A 150 " distance=2.05 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.06 Simple disulfide: pdb=" SG ACYS D 136 " - pdb=" SG ACYS D 150 " distance=2.05 Simple disulfide: pdb=" SG CYS E 409 " - pdb=" SG CYS E 483 " distance=2.06 Simple disulfide: pdb=" SG ACYS H 136 " - pdb=" SG ACYS H 150 " distance=2.05 Simple disulfide: pdb=" SG CYS I 409 " - pdb=" SG CYS I 483 " distance=2.06 Simple disulfide: pdb=" SG ACYS L 136 " - pdb=" SG ACYS L 150 " distance=2.05 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.06 Simple disulfide: pdb=" SG ACYS Q 136 " - pdb=" SG ACYS Q 150 " distance=2.05 Simple disulfide: pdb=" SG CYS R 409 " - pdb=" SG CYS R 483 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA G 3 " - " MAN G 4 " " BMA K 3 " - " MAN K 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA G 3 " - " MAN G 5 " " BMA K 3 " - " MAN K 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG A5405 " - " ASN A 8 " " NAG B 1 " - " ASN A 80 " " NAG C 1 " - " ASN A 149 " " NAG D5405 " - " ASN D 8 " " NAG F 1 " - " ASN D 80 " " NAG G 1 " - " ASN D 149 " " NAG H5405 " - " ASN H 8 " " NAG J 1 " - " ASN H 80 " " NAG K 1 " - " ASN H 149 " " NAG L5405 " - " ASN L 8 " " NAG N 1 " - " ASN L 80 " " NAG P 1 " - " ASN L 149 " " NAG Q5405 " - " ASN Q 8 " " NAG S 1 " - " ASN Q 80 " " NAG T 1 " - " ASN Q 149 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 30 sheets defined 33.6% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.634A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 270 Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 447 removed outlier: 3.930A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'O' and resid 449 through 452 Processing helix chain 'O' and resid 495 through 497 No H-bonds generated for 'chain 'O' and resid 495 through 497' Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 238 removed outlier: 3.634A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 246 through 270 Processing helix chain 'D' and resid 279 through 306 Processing helix chain 'D' and resid 309 through 447 removed outlier: 3.930A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 449 through 452 Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'H' and resid 8 through 21 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 84 through 91 Processing helix chain 'H' and resid 170 through 173 Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 218 through 225 Processing helix chain 'H' and resid 225 through 238 removed outlier: 3.634A pdb=" N TRP H 237 " --> pdb=" O THR H 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 242 Processing helix chain 'H' and resid 246 through 270 Processing helix chain 'H' and resid 279 through 306 Processing helix chain 'H' and resid 309 through 447 removed outlier: 3.930A pdb=" N ILE H 429 " --> pdb=" O ARG H 425 " (cutoff:3.500A) Proline residue: H 432 - end of helix Processing helix chain 'I' and resid 449 through 452 Processing helix chain 'I' and resid 495 through 497 No H-bonds generated for 'chain 'I' and resid 495 through 497' Processing helix chain 'L' and resid 8 through 21 Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 84 through 91 Processing helix chain 'L' and resid 170 through 173 Processing helix chain 'L' and resid 177 through 181 Processing helix chain 'L' and resid 218 through 225 Processing helix chain 'L' and resid 225 through 238 removed outlier: 3.634A pdb=" N TRP L 237 " --> pdb=" O THR L 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL L 238 " --> pdb=" O ILE L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 242 Processing helix chain 'L' and resid 246 through 270 Processing helix chain 'L' and resid 279 through 306 Processing helix chain 'L' and resid 309 through 447 removed outlier: 3.930A pdb=" N ILE L 429 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Proline residue: L 432 - end of helix Processing helix chain 'M' and resid 449 through 452 Processing helix chain 'M' and resid 495 through 497 No H-bonds generated for 'chain 'M' and resid 495 through 497' Processing helix chain 'Q' and resid 8 through 21 Processing helix chain 'Q' and resid 70 through 73 Processing helix chain 'Q' and resid 84 through 91 Processing helix chain 'Q' and resid 170 through 173 Processing helix chain 'Q' and resid 177 through 181 Processing helix chain 'Q' and resid 218 through 225 Processing helix chain 'Q' and resid 225 through 238 removed outlier: 3.634A pdb=" N TRP Q 237 " --> pdb=" O THR Q 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Q 238 " --> pdb=" O ILE Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 242 Processing helix chain 'Q' and resid 246 through 270 Processing helix chain 'Q' and resid 279 through 306 Processing helix chain 'Q' and resid 309 through 447 removed outlier: 3.930A pdb=" N ILE Q 429 " --> pdb=" O ARG Q 425 " (cutoff:3.500A) Proline residue: Q 432 - end of helix Processing helix chain 'R' and resid 449 through 452 Processing helix chain 'R' and resid 495 through 497 No H-bonds generated for 'chain 'R' and resid 495 through 497' Processing sheet with id=1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.462A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR A 60 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE A 47 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA A 45 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN A 64 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP A 43 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR A 66 " --> pdb=" O AASN A 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN A 41 " --> pdb=" O ATYR A 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG A 68 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY A 39 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.883A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 131 " --> pdb=" O ASER A 104 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR A 60 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE A 47 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR A 62 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA A 45 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN A 64 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP A 43 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR A 66 " --> pdb=" O AASN A 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN A 41 " --> pdb=" O ATYR A 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG A 68 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY A 39 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'O' and resid 2 through 7 Processing sheet with id=5, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY O 10 " --> pdb=" O THR O 509 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'O' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY O 10 " --> pdb=" O THR O 509 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS O 483 " --> pdb=" O TRP O 502 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP O 502 " --> pdb=" O CYS O 483 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA O 485 " --> pdb=" O ASP O 500 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.462A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR D 60 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE D 47 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA D 45 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN D 64 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP D 43 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR D 66 " --> pdb=" O AASN D 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN D 41 " --> pdb=" O ATYR D 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG D 68 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY D 39 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.884A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D 131 " --> pdb=" O ASER D 104 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR D 60 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE D 47 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR D 62 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA D 45 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN D 64 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP D 43 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR D 66 " --> pdb=" O AASN D 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN D 41 " --> pdb=" O ATYR D 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG D 68 " --> pdb=" O GLY D 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY D 39 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=11, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY E 10 " --> pdb=" O THR E 509 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE E 420 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG E 425 " --> pdb=" O PHE E 434 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE E 434 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY E 10 " --> pdb=" O THR E 509 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS E 483 " --> pdb=" O TRP E 502 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP E 502 " --> pdb=" O CYS E 483 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA E 485 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 81 through 83 removed outlier: 4.462A pdb=" N ILE H 116 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET H 49 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR H 60 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE H 47 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR H 62 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA H 45 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN H 64 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP H 43 " --> pdb=" O GLN H 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR H 66 " --> pdb=" O AASN H 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN H 41 " --> pdb=" O ATYR H 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG H 68 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY H 39 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.883A pdb=" N THR H 133 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASER H 104 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR H 131 " --> pdb=" O ASER H 104 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL H 106 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG H 129 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET H 49 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR H 60 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE H 47 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR H 62 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA H 45 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN H 64 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP H 43 " --> pdb=" O GLN H 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR H 66 " --> pdb=" O AASN H 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN H 41 " --> pdb=" O ATYR H 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG H 68 " --> pdb=" O GLY H 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY H 39 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER H 156 " --> pdb=" O PRO H 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU H 190 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS H 215 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE H 188 " --> pdb=" O LYS H 215 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'I' and resid 2 through 7 Processing sheet with id=17, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY I 10 " --> pdb=" O THR I 509 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE I 420 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG I 425 " --> pdb=" O PHE I 434 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE I 434 " --> pdb=" O ARG I 425 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY I 10 " --> pdb=" O THR I 509 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS I 483 " --> pdb=" O TRP I 502 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP I 502 " --> pdb=" O CYS I 483 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA I 485 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'L' and resid 81 through 83 removed outlier: 4.462A pdb=" N ILE L 116 " --> pdb=" O LEU L 83 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET L 49 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR L 60 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE L 47 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR L 62 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA L 45 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN L 64 " --> pdb=" O ASP L 43 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP L 43 " --> pdb=" O GLN L 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR L 66 " --> pdb=" O AASN L 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN L 41 " --> pdb=" O ATYR L 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG L 68 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY L 39 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.883A pdb=" N THR L 133 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASER L 104 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR L 131 " --> pdb=" O ASER L 104 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL L 106 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG L 129 " --> pdb=" O VAL L 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET L 49 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR L 60 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE L 47 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR L 62 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA L 45 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN L 64 " --> pdb=" O ASP L 43 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP L 43 " --> pdb=" O GLN L 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR L 66 " --> pdb=" O AASN L 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN L 41 " --> pdb=" O ATYR L 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG L 68 " --> pdb=" O GLY L 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY L 39 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER L 156 " --> pdb=" O PRO L 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU L 190 " --> pdb=" O ARG L 213 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS L 215 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE L 188 " --> pdb=" O LYS L 215 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=23, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY M 10 " --> pdb=" O THR M 509 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS M 483 " --> pdb=" O TRP M 502 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP M 502 " --> pdb=" O CYS M 483 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA M 485 " --> pdb=" O ASP M 500 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'Q' and resid 81 through 83 removed outlier: 4.462A pdb=" N ILE Q 116 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET Q 49 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR Q 60 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE Q 47 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR Q 62 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA Q 45 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN Q 64 " --> pdb=" O ASP Q 43 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP Q 43 " --> pdb=" O GLN Q 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR Q 66 " --> pdb=" O AASN Q 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN Q 41 " --> pdb=" O ATYR Q 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG Q 68 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY Q 39 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.883A pdb=" N THR Q 133 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASER Q 104 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR Q 131 " --> pdb=" O ASER Q 104 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL Q 106 " --> pdb=" O ARG Q 129 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG Q 129 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET Q 49 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR Q 60 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE Q 47 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR Q 62 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA Q 45 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLN Q 64 " --> pdb=" O ASP Q 43 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP Q 43 " --> pdb=" O GLN Q 64 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ATYR Q 66 " --> pdb=" O AASN Q 41 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N AASN Q 41 " --> pdb=" O ATYR Q 66 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ARG Q 68 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLY Q 39 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.700A pdb=" N SER Q 156 " --> pdb=" O PRO Q 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU Q 190 " --> pdb=" O ARG Q 213 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS Q 215 " --> pdb=" O ILE Q 188 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE Q 188 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'R' and resid 2 through 7 Processing sheet with id=29, first strand: chain 'R' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY R 10 " --> pdb=" O THR R 509 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE R 420 " --> pdb=" O LYS R 486 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG R 425 " --> pdb=" O PHE R 434 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE R 434 " --> pdb=" O ARG R 425 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'R' and resid 10 through 11 removed outlier: 7.070A pdb=" N GLY R 10 " --> pdb=" O THR R 509 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS R 483 " --> pdb=" O TRP R 502 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP R 502 " --> pdb=" O CYS R 483 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA R 485 " --> pdb=" O ASP R 500 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3055 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: 3.91 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3302 1.32 - 1.45: 5963 1.45 - 1.57: 11270 1.57 - 1.70: 5 1.70 - 1.83: 190 Bond restraints: 20730 Sorted by residual: bond pdb=" N LEU A 272 " pdb=" CA LEU A 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.91e+01 bond pdb=" N LEU D 272 " pdb=" CA LEU D 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.89e+01 bond pdb=" N LEU Q 272 " pdb=" CA LEU Q 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.88e+01 bond pdb=" N BILE H 164 " pdb=" CA BILE H 164 " ideal model delta sigma weight residual 1.458 1.509 -0.051 1.18e-02 7.18e+03 1.88e+01 bond pdb=" N BILE L 164 " pdb=" CA BILE L 164 " ideal model delta sigma weight residual 1.458 1.508 -0.051 1.18e-02 7.18e+03 1.85e+01 ... (remaining 20725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 20431 1.71 - 3.42: 6844 3.42 - 5.14: 915 5.14 - 6.85: 50 6.85 - 8.56: 10 Bond angle restraints: 28250 Sorted by residual: angle pdb=" CA PHE H 166 " pdb=" CB PHE H 166 " pdb=" CG PHE H 166 " ideal model delta sigma weight residual 113.80 118.54 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" CA PHE A 166 " pdb=" CB PHE A 166 " pdb=" CG PHE A 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE D 166 " pdb=" CB PHE D 166 " pdb=" CG PHE D 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE Q 166 " pdb=" CB PHE Q 166 " pdb=" CG PHE Q 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE L 166 " pdb=" CB PHE L 166 " pdb=" CG PHE L 166 " ideal model delta sigma weight residual 113.80 118.50 -4.70 1.00e+00 1.00e+00 2.21e+01 ... (remaining 28245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10835 17.66 - 35.32: 920 35.32 - 52.99: 135 52.99 - 70.65: 30 70.65 - 88.31: 30 Dihedral angle restraints: 11950 sinusoidal: 4810 harmonic: 7140 Sorted by residual: dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER Q 46 " pdb=" C SER Q 46 " pdb=" N ILE Q 47 " pdb=" CA ILE Q 47 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1325 0.054 - 0.109: 1148 0.109 - 0.163: 537 0.163 - 0.217: 140 0.217 - 0.272: 35 Chirality restraints: 3185 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.33e+01 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.32e+01 chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.29e+01 ... (remaining 3182 not shown) Planarity restraints: 3500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.148 2.00e-02 2.50e+03 7.93e-02 1.26e+02 pdb=" CG TYR A 157 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 157 " -0.148 2.00e-02 2.50e+03 7.92e-02 1.26e+02 pdb=" CG TYR L 157 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR L 157 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR L 157 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR L 157 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR L 157 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR L 157 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR L 157 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 157 " 0.148 2.00e-02 2.50e+03 7.92e-02 1.25e+02 pdb=" CG TYR Q 157 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 157 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 157 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 157 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 157 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR Q 157 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR Q 157 " 0.119 2.00e-02 2.50e+03 ... (remaining 3497 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 10 1.96 - 2.94: 9719 2.94 - 3.92: 62588 3.92 - 4.90: 122849 Warning: very small nonbonded interaction distances. Nonbonded interactions: 195176 Sorted by model distance: nonbonded pdb="CL CL A5409 " pdb="CL CL D5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL H5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL L5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL Q5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL D5409 " pdb="CL CL H5409 " model vdw 0.000 3.340 ... (remaining 195171 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' selection = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'P' 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=0.20 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 22.030 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.014 0.083 20780 Z= 0.979 Angle : 1.610 10.147 28390 Z= 1.160 Chirality : 0.089 0.272 3185 Planarity : 0.018 0.105 3485 Dihedral : 13.746 88.312 7440 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.48 % Allowed : 3.57 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % 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: -0.05 (0.15), residues: 2505 helix: -0.26 (0.17), residues: 675 sheet: 0.75 (0.19), residues: 695 loop : -0.25 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.004 ARG Q 180 TYR 0.148 0.018 TYR A 157 PHE 0.093 0.018 PHE H 63 TRP 0.060 0.015 TRP L 168 HIS 0.034 0.008 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01371 / 0.98 (20730) covalent geometry : angle 1.59329 / 1.16 (28250) SS BOND : bond 0.02364 / 1.62 ( 10) SS BOND : angle 2.29086 / 1.46 ( 20) hydrogen bonds : bond 0.17994 / 11.90 ( 1025) hydrogen bonds : angle 7.31449 / 5.08 ( 3055) link_ALPHA1-3 : bond 0.00677 / 0.42 ( 5) link_ALPHA1-3 : angle 2.75664 / 1.65 ( 15) link_ALPHA1-6 : bond 0.00022 / 0.01 ( 5) link_ALPHA1-6 : angle 4.77991 / 2.96 ( 15) link_BETA1-4 : bond 0.01284 / 0.90 ( 15) link_BETA1-4 : angle 2.99600 / 1.98 ( 45) link_NAG-ASN : bond 0.01131 / 0.72 ( 15) link_NAG-ASN : angle 4.55834 / 3.20 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 307 time to evaluate : 0.669 Fit side-chains REVERT: A 14 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6505 (tt0) REVERT: A 18 LYS cc_start: 0.6858 (tttt) cc_final: 0.6238 (tmmt) REVERT: A 49 MET cc_start: 0.7698 (mtp) cc_final: 0.6724 (pp-130) REVERT: A 137 MET cc_start: 0.8121 (mmp) cc_final: 0.7632 (mmm) REVERT: A 147 GLU cc_start: 0.7456 (tt0) cc_final: 0.7220 (tt0) REVERT: A 213 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7948 (ttp80) REVERT: A 215 LYS cc_start: 0.7759 (tttt) cc_final: 0.7525 (tttm) REVERT: A 227 MET cc_start: 0.7000 (mmt) cc_final: 0.6173 (mtp) REVERT: A 274 LYS cc_start: 0.7509 (mttt) cc_final: 0.7236 (mttp) REVERT: A 282 ASP cc_start: 0.7710 (m-30) cc_final: 0.7475 (m-30) REVERT: A 425 ARG cc_start: 0.6549 (ttt180) cc_final: 0.6061 (ttm110) REVERT: A 433 PHE cc_start: 0.7363 (t80) cc_final: 0.7141 (t80) REVERT: O 423 TRP cc_start: 0.7958 (m100) cc_final: 0.7717 (m100) REVERT: D 14 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6454 (tt0) REVERT: D 18 LYS cc_start: 0.7016 (tttt) cc_final: 0.6359 (tmmt) REVERT: D 48 ASP cc_start: 0.7895 (m-30) cc_final: 0.7396 (m-30) REVERT: D 49 MET cc_start: 0.7754 (mtp) cc_final: 0.6878 (tmm) REVERT: D 138 MET cc_start: 0.8169 (mtt) cc_final: 0.7946 (mtt) REVERT: D 147 GLU cc_start: 0.7399 (tt0) cc_final: 0.7165 (tt0) REVERT: D 173 LYS cc_start: 0.7642 (mttm) cc_final: 0.7439 (mtpt) REVERT: D 227 MET cc_start: 0.6925 (mmt) cc_final: 0.6050 (mtp) REVERT: D 274 LYS cc_start: 0.7408 (mttt) cc_final: 0.7172 (mttp) REVERT: D 301 PHE cc_start: 0.7986 (t80) cc_final: 0.7682 (t80) REVERT: D 425 ARG cc_start: 0.6644 (ttt180) cc_final: 0.6116 (ttm110) REVERT: E 423 TRP cc_start: 0.7943 (m100) cc_final: 0.7719 (m100) REVERT: H 14 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6405 (tt0) REVERT: H 18 LYS cc_start: 0.6836 (tttt) cc_final: 0.6132 (tmmt) REVERT: H 21 LYS cc_start: 0.6448 (tttt) cc_final: 0.6140 (ttmm) REVERT: H 30 ASP cc_start: 0.8392 (m-30) cc_final: 0.8155 (m-30) REVERT: H 49 MET cc_start: 0.7734 (mtp) cc_final: 0.6807 (tmm) REVERT: H 138 MET cc_start: 0.8161 (mtt) cc_final: 0.7925 (mtt) REVERT: H 173 LYS cc_start: 0.7643 (mttm) cc_final: 0.7359 (mtpm) REVERT: H 179 GLU cc_start: 0.7772 (pm20) cc_final: 0.7554 (pm20) REVERT: H 227 MET cc_start: 0.7101 (mmt) cc_final: 0.5989 (ttp) REVERT: H 274 LYS cc_start: 0.7426 (mttt) cc_final: 0.7173 (mttp) REVERT: H 301 PHE cc_start: 0.7967 (t80) cc_final: 0.7574 (t80) REVERT: H 425 ARG cc_start: 0.6641 (ttt180) cc_final: 0.6173 (ttm110) REVERT: H 429 ILE cc_start: 0.6797 (tp) cc_final: 0.6501 (mt) REVERT: H 437 LEU cc_start: 0.7069 (mp) cc_final: 0.6766 (mp) REVERT: L 14 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6420 (tt0) REVERT: L 18 LYS cc_start: 0.6948 (tttt) cc_final: 0.6505 (mtpt) REVERT: L 30 ASP cc_start: 0.8437 (m-30) cc_final: 0.8149 (t0) REVERT: L 49 MET cc_start: 0.7811 (mtp) cc_final: 0.6828 (tmm) REVERT: L 147 GLU cc_start: 0.7528 (tt0) cc_final: 0.7254 (tt0) REVERT: L 227 MET cc_start: 0.6996 (mmt) cc_final: 0.5877 (ttp) REVERT: L 274 LYS cc_start: 0.7497 (mttt) cc_final: 0.7256 (mttp) REVERT: L 301 PHE cc_start: 0.8009 (t80) cc_final: 0.7587 (t80) REVERT: L 425 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6193 (ttm110) REVERT: Q 14 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6385 (tt0) REVERT: Q 18 LYS cc_start: 0.6858 (tttt) cc_final: 0.6198 (tmmt) REVERT: Q 48 ASP cc_start: 0.7828 (m-30) cc_final: 0.7330 (m-30) REVERT: Q 49 MET cc_start: 0.7651 (mtp) cc_final: 0.6712 (tmm) REVERT: Q 147 GLU cc_start: 0.7459 (tt0) cc_final: 0.7162 (tt0) REVERT: Q 213 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7922 (ttp80) REVERT: Q 227 MET cc_start: 0.7066 (mmt) cc_final: 0.6717 (mmp) REVERT: Q 274 LYS cc_start: 0.7437 (mttt) cc_final: 0.7209 (mttp) REVERT: Q 425 ARG cc_start: 0.6737 (ttt180) cc_final: 0.6255 (ttm110) REVERT: R 423 TRP cc_start: 0.7894 (m100) cc_final: 0.7675 (m100) outliers start: 10 outliers final: 5 residues processed: 317 average time/residue: 0.7069 time to fit residues: 249.9266 Evaluate side-chains 270 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 265 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 445 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain I residue 445 THR Chi-restraints excluded: chain M residue 445 THR Chi-restraints excluded: chain R residue 445 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.6839 > 50: distance: 38 - 355: 6.073 distance: 38 - 363: 3.708 distance: 41 - 352: 6.533 distance: 41 - 360: 10.046 distance: 52 - 322: 11.416 distance: 52 - 333: 15.648 distance: 54 - 319: 7.811 distance: 54 - 330: 17.986 distance: 68 - 308: 18.511 distance: 71 - 305: 7.272 distance: 83 - 288: 6.861 distance: 193 - 341: 3.544 distance: 206 - 316: 15.105 distance: 209 - 313: 13.527 distance: 227 - 299: 3.863 distance: 237 - 277: 3.696 distance: 240 - 274: 3.460 distance: 267 - 268: 4.003 distance: 268 - 271: 3.630 distance: 269 - 270: 3.786 distance: 269 - 274: 4.458 distance: 280 - 281: 3.194 distance: 281 - 282: 3.080 distance: 282 - 283: 10.541 distance: 282 - 284: 7.807 distance: 285 - 286: 3.954 distance: 286 - 287: 13.061 distance: 286 - 289: 5.108 distance: 287 - 288: 8.855 distance: 287 - 293: 11.526 distance: 287 - 299: 8.867 distance: 289 - 290: 5.744 distance: 290 - 291: 5.701 distance: 293 - 294: 5.699 distance: 294 - 295: 3.883 distance: 294 - 297: 5.849 distance: 295 - 296: 4.295 distance: 295 - 305: 7.734 distance: 297 - 298: 4.407 distance: 299 - 300: 5.631 distance: 300 - 301: 4.699 distance: 300 - 303: 4.661 distance: 301 - 302: 3.619 distance: 301 - 305: 3.443 distance: 305 - 306: 6.056 distance: 306 - 307: 12.325 distance: 306 - 309: 7.081 distance: 307 - 308: 16.454 distance: 307 - 313: 15.262 distance: 309 - 310: 6.354 distance: 310 - 311: 3.912 distance: 310 - 312: 4.966 distance: 313 - 314: 27.984 distance: 314 - 315: 27.587 distance: 314 - 317: 21.662 distance: 315 - 316: 30.231 distance: 315 - 319: 26.532 distance: 315 - 330: 33.600 distance: 317 - 318: 5.337 distance: 319 - 320: 11.988 distance: 320 - 321: 11.751 distance: 320 - 323: 15.841 distance: 321 - 322: 11.556 distance: 321 - 341: 4.883 distance: 323 - 324: 10.131 distance: 324 - 325: 6.731 distance: 324 - 326: 3.665 distance: 325 - 327: 5.826 distance: 326 - 328: 16.582 distance: 327 - 329: 14.930 distance: 328 - 329: 19.016 distance: 330 - 331: 12.499 distance: 331 - 332: 15.208 distance: 331 - 334: 19.831 distance: 332 - 333: 13.335 distance: 332 - 341: 5.358 distance: 334 - 335: 54.684 distance: 335 - 336: 47.086 distance: 335 - 337: 36.263 distance: 336 - 338: 32.276 distance: 337 - 339: 17.455 distance: 338 - 340: 18.496 distance: 339 - 340: 18.204 distance: 341 - 342: 16.097 distance: 342 - 343: 38.476 distance: 342 - 345: 3.236 distance: 343 - 344: 33.925 distance: 343 - 352: 29.788 distance: 343 - 360: 37.008 distance: 345 - 346: 32.146 distance: 346 - 347: 40.324 distance: 347 - 348: 30.733 distance: 348 - 349: 21.538 distance: 349 - 350: 14.051 distance: 349 - 351: 19.974 distance: 352 - 353: 19.842 distance: 353 - 354: 18.771 distance: 353 - 356: 21.912 distance: 354 - 368: 8.948 distance: 356 - 357: 26.649 distance: 357 - 358: 20.340 distance: 357 - 359: 17.019 distance: 360 - 361: 14.345 distance: 361 - 364: 8.837 distance: 362 - 363: 6.708 distance: 362 - 368: 8.918 distance: 364 - 365: 8.479 distance: 365 - 366: 7.197 distance: 368 - 369: 4.662 distance: 369 - 370: 5.681 distance: 369 - 372: 5.971 distance: 370 - 371: 7.204 distance: 370 - 377: 6.472 distance: 372 - 373: 10.956 distance: 373 - 374: 8.850 distance: 374 - 375: 7.954 distance: 375 - 376: 4.662