Starting phenix.real_space_refine on Fri Sep 19 00:40:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a5v_11657/09_2025/7a5v_11657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a5v_11657/09_2025/7a5v_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 { model { file = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2025/7a5v_11657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2025/7a5v_11657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2025/7a5v_11657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2025/7a5v_11657.map" } 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-2.0-5805/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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: 7.51, per 1000 atoms: 0.35 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: 2.05 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.63 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: 4.69 Time building geometry restraints manager: 2.60 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 - 21.01: 11940 21.01 - 42.03: 645 42.03 - 63.04: 95 63.04 - 84.06: 55 84.06 - 105.07: 25 Dihedral angle restraints: 12760 sinusoidal: 5620 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 12757 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: 4.560 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.880 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 14.871 105.069 8250 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 aren 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 covalent geometry : bond 0.01371 (20730) covalent geometry : angle 1.59329 (28250) SS BOND : bond 0.02364 ( 10) SS BOND : angle 2.29086 ( 20) hydrogen bonds : bond 0.17994 ( 1025) hydrogen bonds : angle 7.31449 ( 3055) link_ALPHA1-3 : bond 0.00677 ( 5) link_ALPHA1-3 : angle 2.75664 ( 15) link_ALPHA1-6 : bond 0.00022 ( 5) link_ALPHA1-6 : angle 4.77991 ( 15) link_BETA1-4 : bond 0.01284 ( 15) link_BETA1-4 : angle 2.99600 ( 45) link_NAG-ASN : bond 0.01131 ( 15) link_NAG-ASN : angle 4.55834 ( 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 : 0.700 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: 0.7474 (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: 0.8148 (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: 0.7179 time to fit residues: 252.6236 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 : 0.691 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN O 461 ASN D 224 GLN H 224 GLN I 461 ASN L 224 GLN Q 224 GLN R 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.188482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.139268 restraints weight = 72377.342| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.74 r_work: 0.3072 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work: 0.2874 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.171 20780 Z= 0.379 Angle : 1.341 23.499 28390 Z= 0.720 Chirality : 0.074 0.819 3185 Planarity : 0.016 0.367 3485 Dihedral : 12.977 113.984 3860 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.69 % Favored : 98.26 % Rotamer: Outliers : 0.76 % Allowed : 6.57 % Favored : 92.67 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: -0.06 (0.16), residues: 2505 helix: -0.50 (0.18), residues: 675 sheet: 0.56 (0.18), residues: 775 loop : 0.00 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.004 ARG E 459 TYR 0.156 0.009 TYR D 157 PHE 0.184 0.010 PHE L 433 TRP 0.125 0.010 TRP D 92 HIS 0.019 0.004 HIS M 414 Details of bonding type rmsd covalent geometry : bond 0.00804 (20730) covalent geometry : angle 1.32049 (28250) SS BOND : bond 0.00835 ( 10) SS BOND : angle 1.48127 ( 20) hydrogen bonds : bond 0.09724 ( 1025) hydrogen bonds : angle 6.36515 ( 3055) link_ALPHA1-3 : bond 0.01423 ( 5) link_ALPHA1-3 : angle 2.94544 ( 15) link_ALPHA1-6 : bond 0.00565 ( 5) link_ALPHA1-6 : angle 4.87721 ( 15) link_BETA1-4 : bond 0.00839 ( 15) link_BETA1-4 : angle 2.47300 ( 45) link_NAG-ASN : bond 0.00812 ( 15) link_NAG-ASN : angle 4.68774 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 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 287 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 275 time to evaluate : 0.616 Fit side-chains REVERT: A 137 MET cc_start: 0.8870 (mmp) cc_final: 0.8539 (mmm) REVERT: A 227 MET cc_start: 0.7961 (mmt) cc_final: 0.7495 (ttm) REVERT: D 48 ASP cc_start: 0.8299 (m-30) cc_final: 0.7977 (m-30) REVERT: D 227 MET cc_start: 0.7792 (mmt) cc_final: 0.7282 (mtp) REVERT: E 470 MET cc_start: 0.5549 (mtp) cc_final: 0.4957 (mtt) REVERT: H 18 LYS cc_start: 0.7502 (tttt) cc_final: 0.7202 (tmmt) REVERT: H 49 MET cc_start: 0.8385 (mtp) cc_final: 0.8084 (tmm) REVERT: H 227 MET cc_start: 0.7975 (mmt) cc_final: 0.7455 (ttm) REVERT: H 301 PHE cc_start: 0.8622 (t80) cc_final: 0.8311 (t80) REVERT: H 437 LEU cc_start: 0.8011 (mp) cc_final: 0.7810 (mp) REVERT: L 227 MET cc_start: 0.7912 (mmt) cc_final: 0.7465 (ttp) REVERT: L 301 PHE cc_start: 0.8687 (t80) cc_final: 0.8384 (t80) REVERT: M 458 SER cc_start: 0.5210 (OUTLIER) cc_final: 0.4464 (p) REVERT: Q 18 LYS cc_start: 0.7568 (tttt) cc_final: 0.7313 (tmmt) REVERT: Q 48 ASP cc_start: 0.8239 (m-30) cc_final: 0.7918 (m-30) REVERT: Q 227 MET cc_start: 0.7941 (mmt) cc_final: 0.7407 (mtp) REVERT: R 423 TRP cc_start: 0.8015 (m100) cc_final: 0.7706 (m100) outliers start: 12 outliers final: 4 residues processed: 283 average time/residue: 0.6799 time to fit residues: 214.6533 Evaluate side-chains 248 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 243 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain M residue 458 SER Chi-restraints excluded: chain Q residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 53 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN E 461 ASN L 224 GLN M 461 ASN Q 224 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.191484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.142349 restraints weight = 98006.216| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.17 r_work: 0.3136 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work: 0.2950 rms_B_bonded: 3.91 restraints_weight: 0.1250 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20780 Z= 0.139 Angle : 0.661 9.259 28390 Z= 0.351 Chirality : 0.047 0.172 3185 Planarity : 0.005 0.098 3485 Dihedral : 10.243 77.399 3856 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.52 % Allowed : 6.76 % Favored : 92.71 % 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 aren not related in a simple way. whole: 1.31 (0.16), residues: 2505 helix: 1.45 (0.19), residues: 685 sheet: 0.93 (0.18), residues: 760 loop : 0.60 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 213 TYR 0.029 0.002 TYR A 299 PHE 0.020 0.002 PHE Q 221 TRP 0.011 0.002 TRP Q 168 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00277 (20730) covalent geometry : angle 0.64346 (28250) SS BOND : bond 0.00371 ( 10) SS BOND : angle 0.62035 ( 20) hydrogen bonds : bond 0.05362 ( 1025) hydrogen bonds : angle 5.05421 ( 3055) link_ALPHA1-3 : bond 0.01044 ( 5) link_ALPHA1-3 : angle 1.39324 ( 15) link_ALPHA1-6 : bond 0.00720 ( 5) link_ALPHA1-6 : angle 1.31408 ( 15) link_BETA1-4 : bond 0.00498 ( 15) link_BETA1-4 : angle 2.24045 ( 45) link_NAG-ASN : bond 0.00279 ( 15) link_NAG-ASN : angle 3.06659 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 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 282 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 272 time to evaluate : 0.464 Fit side-chains REVERT: A 137 MET cc_start: 0.8808 (mmp) cc_final: 0.8467 (mmm) REVERT: A 227 MET cc_start: 0.7899 (mmt) cc_final: 0.7348 (ttm) REVERT: D 48 ASP cc_start: 0.8217 (m-30) cc_final: 0.7921 (m-30) REVERT: D 70 LYS cc_start: 0.8888 (mttp) cc_final: 0.8633 (mppt) REVERT: D 227 MET cc_start: 0.7881 (mmt) cc_final: 0.7370 (mtp) REVERT: E 470 MET cc_start: 0.5566 (mtp) cc_final: 0.5039 (mtt) REVERT: H 18 LYS cc_start: 0.7518 (tttt) cc_final: 0.7149 (tmmt) REVERT: H 49 MET cc_start: 0.8229 (mtp) cc_final: 0.7917 (tmm) REVERT: H 227 MET cc_start: 0.7923 (mmt) cc_final: 0.7360 (ttp) REVERT: I 438 ILE cc_start: 0.7421 (tp) cc_final: 0.7202 (tt) REVERT: L 227 MET cc_start: 0.7946 (mmt) cc_final: 0.7384 (ttp) REVERT: L 268 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6429 (tt) REVERT: Q 18 LYS cc_start: 0.7513 (tttt) cc_final: 0.7277 (tmmt) REVERT: Q 48 ASP cc_start: 0.8070 (m-30) cc_final: 0.7775 (m-30) REVERT: Q 227 MET cc_start: 0.7876 (mmt) cc_final: 0.7608 (mmp) REVERT: R 423 TRP cc_start: 0.7884 (m100) cc_final: 0.7575 (m100) outliers start: 10 outliers final: 2 residues processed: 275 average time/residue: 0.6848 time to fit residues: 210.8253 Evaluate side-chains 260 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 257 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 420 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 37 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN H 90 GLN H 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.188712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.139213 restraints weight = 98814.342| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.15 r_work: 0.3094 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work: 0.2892 rms_B_bonded: 3.95 restraints_weight: 0.1250 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20780 Z= 0.198 Angle : 0.755 11.171 28390 Z= 0.400 Chirality : 0.051 0.184 3185 Planarity : 0.006 0.062 3485 Dihedral : 10.521 79.650 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.86 % Allowed : 6.71 % Favored : 92.43 % 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 aren not related in a simple way. whole: 1.53 (0.16), residues: 2505 helix: 1.69 (0.19), residues: 685 sheet: 0.97 (0.18), residues: 785 loop : 0.76 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 28 TYR 0.033 0.003 TYR L 299 PHE 0.025 0.003 PHE A 221 TRP 0.012 0.002 TRP D 168 HIS 0.009 0.002 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00416 (20730) covalent geometry : angle 0.73492 (28250) SS BOND : bond 0.00581 ( 10) SS BOND : angle 1.00387 ( 20) hydrogen bonds : bond 0.06170 ( 1025) hydrogen bonds : angle 5.20325 ( 3055) link_ALPHA1-3 : bond 0.00881 ( 5) link_ALPHA1-3 : angle 1.17639 ( 15) link_ALPHA1-6 : bond 0.00625 ( 5) link_ALPHA1-6 : angle 1.93102 ( 15) link_BETA1-4 : bond 0.00482 ( 15) link_BETA1-4 : angle 2.53838 ( 45) link_NAG-ASN : bond 0.00527 ( 15) link_NAG-ASN : angle 3.52571 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 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 273 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 258 time to evaluate : 0.752 Fit side-chains REVERT: A 49 MET cc_start: 0.8335 (ptt) cc_final: 0.8055 (pp-130) REVERT: A 137 MET cc_start: 0.8825 (mmp) cc_final: 0.8480 (mmm) REVERT: A 227 MET cc_start: 0.7899 (mmt) cc_final: 0.7324 (ttm) REVERT: D 48 ASP cc_start: 0.8250 (m-30) cc_final: 0.7932 (m-30) REVERT: D 227 MET cc_start: 0.7915 (mmt) cc_final: 0.7375 (ttp) REVERT: H 18 LYS cc_start: 0.7567 (tttt) cc_final: 0.7188 (tmmt) REVERT: H 49 MET cc_start: 0.8237 (mtp) cc_final: 0.7917 (tmm) REVERT: H 227 MET cc_start: 0.7969 (mmt) cc_final: 0.7384 (ttp) REVERT: H 268 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6421 (tt) REVERT: L 227 MET cc_start: 0.8042 (mmt) cc_final: 0.7420 (ttp) REVERT: L 268 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6363 (tt) REVERT: Q 18 LYS cc_start: 0.7572 (tttt) cc_final: 0.7281 (tmmt) REVERT: Q 48 ASP cc_start: 0.8197 (m-30) cc_final: 0.7870 (m-30) REVERT: Q 227 MET cc_start: 0.7907 (mmt) cc_final: 0.7343 (mtp) outliers start: 15 outliers final: 3 residues processed: 265 average time/residue: 0.7231 time to fit residues: 214.5142 Evaluate side-chains 259 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 254 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 483 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 185 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 146 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN H 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.190451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.141365 restraints weight = 100111.473| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 4.33 r_work: 0.3120 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work: 0.2922 rms_B_bonded: 4.15 restraints_weight: 0.1250 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20780 Z= 0.140 Angle : 0.643 7.408 28390 Z= 0.341 Chirality : 0.047 0.171 3185 Planarity : 0.004 0.040 3485 Dihedral : 9.730 74.644 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.76 % Allowed : 7.19 % Favored : 92.05 % 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 aren not related in a simple way. whole: 1.76 (0.16), residues: 2505 helix: 1.95 (0.19), residues: 685 sheet: 1.11 (0.18), residues: 780 loop : 0.84 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 213 TYR 0.030 0.002 TYR L 299 PHE 0.019 0.002 PHE A 221 TRP 0.010 0.001 TRP E 423 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00284 (20730) covalent geometry : angle 0.62430 (28250) SS BOND : bond 0.00386 ( 10) SS BOND : angle 0.67192 ( 20) hydrogen bonds : bond 0.05240 ( 1025) hydrogen bonds : angle 4.87777 ( 3055) link_ALPHA1-3 : bond 0.00963 ( 5) link_ALPHA1-3 : angle 1.30342 ( 15) link_ALPHA1-6 : bond 0.00666 ( 5) link_ALPHA1-6 : angle 1.41883 ( 15) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 2.23536 ( 45) link_NAG-ASN : bond 0.00320 ( 15) link_NAG-ASN : angle 3.11387 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 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 276 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 0.650 Fit side-chains REVERT: A 49 MET cc_start: 0.8388 (ptt) cc_final: 0.8078 (pp-130) REVERT: A 137 MET cc_start: 0.8855 (mmp) cc_final: 0.8540 (mmm) REVERT: A 227 MET cc_start: 0.7839 (mmt) cc_final: 0.7189 (ttp) REVERT: D 48 ASP cc_start: 0.8223 (m-30) cc_final: 0.7905 (m-30) REVERT: D 49 MET cc_start: 0.8330 (ptt) cc_final: 0.8018 (pp-130) REVERT: D 227 MET cc_start: 0.7877 (mmt) cc_final: 0.7310 (ttp) REVERT: H 18 LYS cc_start: 0.7548 (tttt) cc_final: 0.7166 (tmmt) REVERT: H 49 MET cc_start: 0.8253 (mtp) cc_final: 0.7961 (pp-130) REVERT: H 227 MET cc_start: 0.7900 (mmt) cc_final: 0.7276 (ttp) REVERT: H 268 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6304 (tt) REVERT: I 438 ILE cc_start: 0.7434 (tp) cc_final: 0.7232 (tt) REVERT: L 49 MET cc_start: 0.8386 (ptt) cc_final: 0.8135 (pp-130) REVERT: L 227 MET cc_start: 0.7927 (mmt) cc_final: 0.7347 (ttp) REVERT: L 268 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6243 (tt) REVERT: Q 18 LYS cc_start: 0.7549 (tttt) cc_final: 0.7279 (tmmt) REVERT: Q 213 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8497 (mtm-85) REVERT: Q 227 MET cc_start: 0.7819 (mmt) cc_final: 0.7243 (mtp) outliers start: 14 outliers final: 6 residues processed: 267 average time/residue: 0.6749 time to fit residues: 201.7232 Evaluate side-chains 268 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 260 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 62 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 200 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN H 224 GLN L 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.190489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.141255 restraints weight = 102563.316| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 4.29 r_work: 0.3127 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work: 0.2932 rms_B_bonded: 3.88 restraints_weight: 0.1250 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20780 Z= 0.140 Angle : 0.644 7.579 28390 Z= 0.339 Chirality : 0.047 0.183 3185 Planarity : 0.004 0.038 3485 Dihedral : 9.138 69.301 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.67 % Allowed : 7.38 % Favored : 91.95 % 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 aren not related in a simple way. whole: 1.80 (0.16), residues: 2505 helix: 1.97 (0.19), residues: 685 sheet: 1.07 (0.18), residues: 790 loop : 0.94 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 141 TYR 0.031 0.002 TYR L 299 PHE 0.019 0.002 PHE Q 221 TRP 0.012 0.001 TRP I 423 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00283 (20730) covalent geometry : angle 0.62550 (28250) SS BOND : bond 0.00384 ( 10) SS BOND : angle 0.73837 ( 20) hydrogen bonds : bond 0.05185 ( 1025) hydrogen bonds : angle 4.81560 ( 3055) link_ALPHA1-3 : bond 0.00974 ( 5) link_ALPHA1-3 : angle 1.39615 ( 15) link_ALPHA1-6 : bond 0.00820 ( 5) link_ALPHA1-6 : angle 1.34851 ( 15) link_BETA1-4 : bond 0.00365 ( 15) link_BETA1-4 : angle 2.16608 ( 45) link_NAG-ASN : bond 0.00355 ( 15) link_NAG-ASN : angle 3.08147 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 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 278 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 267 time to evaluate : 0.742 Fit side-chains REVERT: A 49 MET cc_start: 0.8362 (ptt) cc_final: 0.8062 (pp-130) REVERT: A 227 MET cc_start: 0.7835 (mmt) cc_final: 0.7207 (ttp) REVERT: D 48 ASP cc_start: 0.8185 (m-30) cc_final: 0.7855 (m-30) REVERT: D 49 MET cc_start: 0.8282 (ptt) cc_final: 0.7991 (pp-130) REVERT: D 227 MET cc_start: 0.7883 (mmt) cc_final: 0.7328 (ttp) REVERT: D 425 ARG cc_start: 0.7491 (ttm110) cc_final: 0.7252 (mtm-85) REVERT: H 18 LYS cc_start: 0.7539 (tttt) cc_final: 0.7158 (tmmt) REVERT: H 49 MET cc_start: 0.8150 (mtp) cc_final: 0.7921 (pp-130) REVERT: H 213 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8383 (mtm-85) REVERT: H 227 MET cc_start: 0.7889 (mmt) cc_final: 0.7302 (ttp) REVERT: H 268 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6464 (tt) REVERT: L 49 MET cc_start: 0.8379 (ptt) cc_final: 0.8165 (pp-130) REVERT: L 227 MET cc_start: 0.7880 (mmt) cc_final: 0.7302 (ttp) REVERT: L 268 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6314 (tt) REVERT: Q 18 LYS cc_start: 0.7534 (tttt) cc_final: 0.7144 (tmmt) REVERT: Q 227 MET cc_start: 0.7808 (mmt) cc_final: 0.7524 (mmp) outliers start: 11 outliers final: 6 residues processed: 272 average time/residue: 0.7036 time to fit residues: 214.0609 Evaluate side-chains 271 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 263 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 188 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN L 224 GLN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.190730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.141407 restraints weight = 106254.242| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.30 r_work: 0.3120 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work: 0.2932 rms_B_bonded: 3.92 restraints_weight: 0.1250 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20780 Z= 0.141 Angle : 0.645 7.486 28390 Z= 0.339 Chirality : 0.047 0.208 3185 Planarity : 0.004 0.038 3485 Dihedral : 8.797 65.181 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.81 % Allowed : 7.71 % Favored : 91.48 % 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 aren not related in a simple way. whole: 1.80 (0.16), residues: 2505 helix: 1.93 (0.19), residues: 685 sheet: 1.19 (0.18), residues: 765 loop : 0.87 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 213 TYR 0.031 0.002 TYR L 299 PHE 0.018 0.002 PHE Q 221 TRP 0.013 0.001 TRP I 423 HIS 0.005 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00286 (20730) covalent geometry : angle 0.62742 (28250) SS BOND : bond 0.00387 ( 10) SS BOND : angle 0.78158 ( 20) hydrogen bonds : bond 0.05153 ( 1025) hydrogen bonds : angle 4.78633 ( 3055) link_ALPHA1-3 : bond 0.01018 ( 5) link_ALPHA1-3 : angle 1.43316 ( 15) link_ALPHA1-6 : bond 0.00933 ( 5) link_ALPHA1-6 : angle 1.20941 ( 15) link_BETA1-4 : bond 0.00369 ( 15) link_BETA1-4 : angle 2.10789 ( 45) link_NAG-ASN : bond 0.00338 ( 15) link_NAG-ASN : angle 3.08166 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 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 277 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 0.663 Fit side-chains REVERT: A 49 MET cc_start: 0.8372 (ptt) cc_final: 0.8066 (pp-130) REVERT: A 70 LYS cc_start: 0.8565 (mttp) cc_final: 0.8241 (mppt) REVERT: A 227 MET cc_start: 0.7786 (mmt) cc_final: 0.7155 (ttp) REVERT: O 459 ARG cc_start: 0.4797 (OUTLIER) cc_final: 0.4562 (pmt170) REVERT: D 48 ASP cc_start: 0.8201 (m-30) cc_final: 0.7866 (m-30) REVERT: D 49 MET cc_start: 0.8298 (ptt) cc_final: 0.7995 (pp-130) REVERT: D 227 MET cc_start: 0.7873 (mmt) cc_final: 0.7325 (ttp) REVERT: D 425 ARG cc_start: 0.7528 (ttm110) cc_final: 0.7290 (mtm-85) REVERT: H 18 LYS cc_start: 0.7555 (tttt) cc_final: 0.7175 (tmmt) REVERT: H 49 MET cc_start: 0.8164 (mtp) cc_final: 0.7953 (pp-130) REVERT: H 227 MET cc_start: 0.7905 (mmt) cc_final: 0.7317 (ttp) REVERT: H 268 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6409 (tt) REVERT: L 49 MET cc_start: 0.8434 (ptt) cc_final: 0.8208 (pp-130) REVERT: L 227 MET cc_start: 0.7887 (mmt) cc_final: 0.7319 (ttp) REVERT: L 268 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6344 (tt) REVERT: Q 18 LYS cc_start: 0.7597 (tttt) cc_final: 0.7208 (tmmt) REVERT: Q 213 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8498 (mtm-85) REVERT: Q 227 MET cc_start: 0.7816 (mmt) cc_final: 0.7244 (mtp) outliers start: 14 outliers final: 7 residues processed: 270 average time/residue: 0.6515 time to fit residues: 196.6361 Evaluate side-chains 271 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 261 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 470 MET Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 192 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 181 optimal weight: 0.2980 chunk 137 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 GLN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.189900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.140402 restraints weight = 101795.053| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.20 r_work: 0.3114 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work: 0.2919 rms_B_bonded: 3.83 restraints_weight: 0.1250 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20780 Z= 0.161 Angle : 0.688 8.169 28390 Z= 0.361 Chirality : 0.049 0.219 3185 Planarity : 0.005 0.047 3485 Dihedral : 8.868 64.150 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.90 % Allowed : 7.57 % Favored : 91.52 % 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 aren not related in a simple way. whole: 1.76 (0.16), residues: 2505 helix: 1.81 (0.19), residues: 685 sheet: 1.11 (0.18), residues: 800 loop : 0.95 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 141 TYR 0.032 0.002 TYR L 299 PHE 0.020 0.002 PHE Q 221 TRP 0.015 0.002 TRP R 423 HIS 0.006 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00332 (20730) covalent geometry : angle 0.66933 (28250) SS BOND : bond 0.00466 ( 10) SS BOND : angle 0.97487 ( 20) hydrogen bonds : bond 0.05504 ( 1025) hydrogen bonds : angle 4.89631 ( 3055) link_ALPHA1-3 : bond 0.01014 ( 5) link_ALPHA1-3 : angle 1.44816 ( 15) link_ALPHA1-6 : bond 0.00945 ( 5) link_ALPHA1-6 : angle 1.30694 ( 15) link_BETA1-4 : bond 0.00405 ( 15) link_BETA1-4 : angle 2.22146 ( 45) link_NAG-ASN : bond 0.00418 ( 15) link_NAG-ASN : angle 3.26071 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 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 275 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 259 time to evaluate : 0.658 Fit side-chains REVERT: A 49 MET cc_start: 0.8373 (ptt) cc_final: 0.8052 (pp-130) REVERT: A 227 MET cc_start: 0.7837 (mmt) cc_final: 0.7197 (ttp) REVERT: O 459 ARG cc_start: 0.4894 (OUTLIER) cc_final: 0.4668 (pmt170) REVERT: D 48 ASP cc_start: 0.8172 (m-30) cc_final: 0.7826 (m-30) REVERT: D 49 MET cc_start: 0.8267 (ptt) cc_final: 0.7949 (pp-130) REVERT: D 227 MET cc_start: 0.7876 (mmt) cc_final: 0.7345 (ttp) REVERT: H 18 LYS cc_start: 0.7545 (tttt) cc_final: 0.7336 (mtpt) REVERT: H 49 MET cc_start: 0.8175 (mtp) cc_final: 0.7925 (pp-130) REVERT: H 227 MET cc_start: 0.7926 (mmt) cc_final: 0.7348 (ttp) REVERT: H 268 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6492 (tt) REVERT: I 438 ILE cc_start: 0.7454 (tp) cc_final: 0.7253 (tt) REVERT: L 49 MET cc_start: 0.8440 (ptt) cc_final: 0.8174 (pp-130) REVERT: L 227 MET cc_start: 0.7963 (mmt) cc_final: 0.7356 (ttp) REVERT: Q 18 LYS cc_start: 0.7613 (tttt) cc_final: 0.7259 (tmmt) REVERT: Q 227 MET cc_start: 0.7876 (mmt) cc_final: 0.7303 (mtp) outliers start: 16 outliers final: 10 residues processed: 269 average time/residue: 0.6623 time to fit residues: 199.3775 Evaluate side-chains 270 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 258 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain M residue 470 MET Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 220 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN H 41 ASN B H 90 GLN L 224 GLN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 461 ASN Q 224 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.188007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.138635 restraints weight = 106884.730| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 4.24 r_work: 0.3093 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work: 0.2890 rms_B_bonded: 3.88 restraints_weight: 0.1250 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20780 Z= 0.252 Angle : 0.838 9.416 28390 Z= 0.441 Chirality : 0.054 0.251 3185 Planarity : 0.006 0.066 3485 Dihedral : 9.730 68.897 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.05 % Allowed : 7.57 % Favored : 91.38 % 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 aren not related in a simple way. whole: 1.54 (0.16), residues: 2505 helix: 1.41 (0.19), residues: 685 sheet: 1.09 (0.18), residues: 795 loop : 0.90 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Q 28 TYR 0.036 0.004 TYR D 157 PHE 0.033 0.003 PHE L 98 TRP 0.020 0.003 TRP R 423 HIS 0.012 0.002 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00540 (20730) covalent geometry : angle 0.81702 (28250) SS BOND : bond 0.00720 ( 10) SS BOND : angle 1.54033 ( 20) hydrogen bonds : bond 0.06585 ( 1025) hydrogen bonds : angle 5.26222 ( 3055) link_ALPHA1-3 : bond 0.00899 ( 5) link_ALPHA1-3 : angle 1.55605 ( 15) link_ALPHA1-6 : bond 0.00887 ( 5) link_ALPHA1-6 : angle 1.99674 ( 15) link_BETA1-4 : bond 0.00571 ( 15) link_BETA1-4 : angle 2.64847 ( 45) link_NAG-ASN : bond 0.00692 ( 15) link_NAG-ASN : angle 3.72047 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 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 270 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 253 time to evaluate : 0.677 Fit side-chains REVERT: A 49 MET cc_start: 0.8353 (ptt) cc_final: 0.8020 (pp-130) REVERT: A 227 MET cc_start: 0.7871 (mmt) cc_final: 0.7278 (ttm) REVERT: O 459 ARG cc_start: 0.5014 (OUTLIER) cc_final: 0.3582 (ppt170) REVERT: D 48 ASP cc_start: 0.8205 (m-30) cc_final: 0.7854 (m-30) REVERT: D 49 MET cc_start: 0.8250 (ptt) cc_final: 0.7905 (pp-130) REVERT: D 227 MET cc_start: 0.7858 (mmt) cc_final: 0.7348 (ttp) REVERT: H 18 LYS cc_start: 0.7558 (tttt) cc_final: 0.7204 (tmmt) REVERT: H 49 MET cc_start: 0.8203 (mtp) cc_final: 0.7903 (pp-130) REVERT: H 227 MET cc_start: 0.7879 (mmt) cc_final: 0.7270 (ttp) REVERT: H 268 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6533 (tt) REVERT: I 458 SER cc_start: 0.4952 (OUTLIER) cc_final: 0.4643 (p) REVERT: L 49 MET cc_start: 0.8489 (ptt) cc_final: 0.8172 (pp-130) REVERT: L 227 MET cc_start: 0.7899 (mmt) cc_final: 0.7311 (ttp) REVERT: Q 18 LYS cc_start: 0.7670 (tttt) cc_final: 0.7315 (tmmt) REVERT: Q 227 MET cc_start: 0.7829 (mmt) cc_final: 0.7269 (mtp) REVERT: R 459 ARG cc_start: 0.4788 (OUTLIER) cc_final: 0.3352 (ppt170) outliers start: 17 outliers final: 10 residues processed: 262 average time/residue: 0.6786 time to fit residues: 198.6246 Evaluate side-chains 266 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain I residue 458 SER Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 470 MET Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 459 ARG Chi-restraints excluded: chain R residue 470 MET Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 GLN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.189236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139702 restraints weight = 104248.811| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.22 r_work: 0.3109 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work: 0.2909 rms_B_bonded: 3.89 restraints_weight: 0.1250 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20780 Z= 0.184 Angle : 0.728 9.674 28390 Z= 0.383 Chirality : 0.050 0.206 3185 Planarity : 0.005 0.051 3485 Dihedral : 9.516 68.319 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.76 % Allowed : 7.86 % Favored : 91.38 % 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 aren not related in a simple way. whole: 1.64 (0.16), residues: 2505 helix: 1.61 (0.19), residues: 685 sheet: 1.11 (0.18), residues: 795 loop : 0.89 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 213 TYR 0.030 0.003 TYR A 299 PHE 0.021 0.002 PHE Q 221 TRP 0.019 0.002 TRP R 423 HIS 0.008 0.002 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00386 (20730) covalent geometry : angle 0.70922 (28250) SS BOND : bond 0.00526 ( 10) SS BOND : angle 1.03980 ( 20) hydrogen bonds : bond 0.05802 ( 1025) hydrogen bonds : angle 5.04656 ( 3055) link_ALPHA1-3 : bond 0.00994 ( 5) link_ALPHA1-3 : angle 1.32444 ( 15) link_ALPHA1-6 : bond 0.00822 ( 5) link_ALPHA1-6 : angle 1.33375 ( 15) link_BETA1-4 : bond 0.00463 ( 15) link_BETA1-4 : angle 2.35639 ( 45) link_NAG-ASN : bond 0.00479 ( 15) link_NAG-ASN : angle 3.38235 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 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 271 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 260 time to evaluate : 0.655 Fit side-chains REVERT: A 49 MET cc_start: 0.8403 (ptt) cc_final: 0.8089 (pp-130) REVERT: A 227 MET cc_start: 0.7883 (mmt) cc_final: 0.7272 (ttm) REVERT: O 459 ARG cc_start: 0.4840 (OUTLIER) cc_final: 0.3465 (ppt170) REVERT: D 48 ASP cc_start: 0.8224 (m-30) cc_final: 0.7888 (m-30) REVERT: D 49 MET cc_start: 0.8277 (ptt) cc_final: 0.7969 (pp-130) REVERT: D 227 MET cc_start: 0.7867 (mmt) cc_final: 0.7347 (ttp) REVERT: H 18 LYS cc_start: 0.7557 (tttt) cc_final: 0.7174 (tmmt) REVERT: H 49 MET cc_start: 0.8249 (mtp) cc_final: 0.7969 (pp-130) REVERT: H 227 MET cc_start: 0.7940 (mmt) cc_final: 0.7345 (ttp) REVERT: H 268 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6464 (tt) REVERT: L 49 MET cc_start: 0.8441 (ptt) cc_final: 0.8175 (pp-130) REVERT: L 227 MET cc_start: 0.7926 (mmt) cc_final: 0.7332 (ttp) REVERT: Q 18 LYS cc_start: 0.7664 (tttt) cc_final: 0.7353 (tmmt) REVERT: Q 227 MET cc_start: 0.7858 (mmt) cc_final: 0.7290 (mtp) outliers start: 11 outliers final: 9 residues processed: 265 average time/residue: 0.6460 time to fit residues: 191.8162 Evaluate side-chains 270 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 259 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain M residue 470 MET Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 8 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 94 optimal weight: 0.0470 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 GLN L 265 ASN Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.190526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.141289 restraints weight = 105438.891| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.18 r_work: 0.3126 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work: 0.2927 rms_B_bonded: 3.98 restraints_weight: 0.1250 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20780 Z= 0.147 Angle : 0.665 9.412 28390 Z= 0.348 Chirality : 0.048 0.215 3185 Planarity : 0.004 0.040 3485 Dihedral : 9.030 65.280 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.86 % Allowed : 7.86 % Favored : 91.29 % 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 aren not related in a simple way. whole: 1.73 (0.16), residues: 2505 helix: 1.79 (0.19), residues: 685 sheet: 1.20 (0.18), residues: 775 loop : 0.84 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 213 TYR 0.031 0.002 TYR H 299 PHE 0.019 0.002 PHE Q 221 TRP 0.019 0.002 TRP R 423 HIS 0.005 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00300 (20730) covalent geometry : angle 0.64806 (28250) SS BOND : bond 0.00386 ( 10) SS BOND : angle 0.86006 ( 20) hydrogen bonds : bond 0.05222 ( 1025) hydrogen bonds : angle 4.85480 ( 3055) link_ALPHA1-3 : bond 0.01053 ( 5) link_ALPHA1-3 : angle 1.31493 ( 15) link_ALPHA1-6 : bond 0.00899 ( 5) link_ALPHA1-6 : angle 1.23884 ( 15) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 2.11498 ( 45) link_NAG-ASN : bond 0.00379 ( 15) link_NAG-ASN : angle 3.09640 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18726.03 seconds wall clock time: 316 minutes 44.50 seconds (19004.50 seconds total)