Starting phenix.real_space_refine on Sun Sep 13 07:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a5v_11657/09_2026/7a5v_11657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a5v_11657/09_2026/7a5v_11657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2026/7a5v_11657.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2026/7a5v_11657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2026/7a5v_11657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2026/7a5v_11657.map" model { file = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2026/7a5v_11657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a5v_11657/09_2026/7a5v_11657.cif" } resolution = 1.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 115 5.16 5 Cl 10 4.86 5 C 13175 2.51 5 N 3190 2.21 5 O 4665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21155 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "O" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "Q" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "R" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 105 residue: pdb=" N AMET A 40 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 40 " occ=0.50 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ATYR A 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 66 " occ=0.50 residue: pdb=" N AASN A 85 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 85 " occ=0.50 residue: pdb=" N ASER A 104 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 104 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N AILE A 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 164 " occ=0.50 residue: pdb=" N AVAL A 198 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 198 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N APHE A 212 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 212 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N ATHR A 225 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 225 " occ=0.50 ... (remaining 93 not shown) Time building chain proxies: 7.30, 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: 2.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 30 sheets defined 33.6% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 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: 4.65 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3302 1.32 - 1.45: 5963 1.45 - 1.57: 11270 1.57 - 1.70: 5 1.70 - 1.83: 190 Bond restraints: 20730 Sorted by residual: bond pdb=" N LEU A 272 " pdb=" CA LEU A 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.91e+01 bond pdb=" N LEU D 272 " pdb=" CA LEU D 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.89e+01 bond pdb=" N LEU Q 272 " pdb=" CA LEU Q 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.88e+01 bond pdb=" N BILE H 164 " pdb=" CA BILE H 164 " ideal model delta sigma weight residual 1.458 1.509 -0.051 1.18e-02 7.18e+03 1.88e+01 bond pdb=" N BILE L 164 " pdb=" CA BILE L 164 " ideal model delta sigma weight residual 1.458 1.508 -0.051 1.18e-02 7.18e+03 1.85e+01 ... (remaining 20725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 20431 1.71 - 3.42: 6844 3.42 - 5.14: 915 5.14 - 6.85: 50 6.85 - 8.56: 10 Bond angle restraints: 28250 Sorted by residual: angle pdb=" CA PHE H 166 " pdb=" CB PHE H 166 " pdb=" CG PHE H 166 " ideal model delta sigma weight residual 113.80 118.54 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" CA PHE A 166 " pdb=" CB PHE A 166 " pdb=" CG PHE A 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE D 166 " pdb=" CB PHE D 166 " pdb=" CG PHE D 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE Q 166 " pdb=" CB PHE Q 166 " pdb=" CG PHE Q 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE L 166 " pdb=" CB PHE L 166 " pdb=" CG PHE L 166 " ideal model delta sigma weight residual 113.80 118.50 -4.70 1.00e+00 1.00e+00 2.21e+01 ... (remaining 28245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10835 17.66 - 35.32: 920 35.32 - 52.99: 135 52.99 - 70.65: 30 70.65 - 88.31: 30 Dihedral angle restraints: 11950 sinusoidal: 4810 harmonic: 7140 Sorted by residual: dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER Q 46 " pdb=" C SER Q 46 " pdb=" N ILE Q 47 " pdb=" CA ILE Q 47 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1325 0.054 - 0.109: 1148 0.109 - 0.163: 537 0.163 - 0.217: 140 0.217 - 0.272: 35 Chirality restraints: 3185 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.33e+01 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.32e+01 chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.29e+01 ... (remaining 3182 not shown) Planarity restraints: 3500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.148 2.00e-02 2.50e+03 7.93e-02 1.26e+02 pdb=" CG TYR A 157 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 157 " -0.148 2.00e-02 2.50e+03 7.92e-02 1.26e+02 pdb=" CG TYR L 157 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR L 157 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR L 157 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR L 157 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR L 157 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR L 157 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR L 157 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 157 " 0.148 2.00e-02 2.50e+03 7.92e-02 1.25e+02 pdb=" CG TYR Q 157 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 157 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 157 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 157 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 157 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR Q 157 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR Q 157 " 0.119 2.00e-02 2.50e+03 ... (remaining 3497 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 10 1.96 - 2.94: 9719 2.94 - 3.92: 62588 3.92 - 4.90: 122849 Warning: very small nonbonded interaction distances. Nonbonded interactions: 195176 Sorted by model distance: nonbonded pdb="CL CL A5409 " pdb="CL CL D5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL H5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL L5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL Q5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL D5409 " pdb="CL CL H5409 " model vdw 0.000 3.340 ... (remaining 195171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.010 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.083 20780 Z= 0.979 Angle : 1.610 10.147 28390 Z= 1.160 Chirality : 0.089 0.272 3185 Planarity : 0.018 0.105 3485 Dihedral : 13.746 88.312 7440 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.48 % Allowed : 3.57 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 2505 helix: -0.26 (0.17), residues: 675 sheet: 0.75 (0.19), residues: 695 loop : -0.25 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.004 ARG Q 180 TYR 0.148 0.018 TYR A 157 PHE 0.093 0.018 PHE H 63 TRP 0.060 0.015 TRP L 168 HIS 0.034 0.008 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01371 / 0.98 (20730) covalent geometry : angle 1.59329 / 1.16 (28250) SS BOND : bond 0.02364 / 1.62 ( 10) SS BOND : angle 2.29086 / 1.46 ( 20) hydrogen bonds : bond 0.17994 / 11.90 ( 1025) hydrogen bonds : angle 7.31449 / 5.08 ( 3055) link_ALPHA1-3 : bond 0.00677 / 0.42 ( 5) link_ALPHA1-3 : angle 2.75664 / 1.65 ( 15) link_ALPHA1-6 : bond 0.00022 / 0.01 ( 5) link_ALPHA1-6 : angle 4.77991 / 2.96 ( 15) link_BETA1-4 : bond 0.01284 / 0.90 ( 15) link_BETA1-4 : angle 2.99600 / 1.98 ( 45) link_NAG-ASN : bond 0.01131 / 0.72 ( 15) link_NAG-ASN : angle 4.55834 / 3.20 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 307 time to evaluate : 0.843 Fit side-chains REVERT: A 14 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6505 (tt0) REVERT: A 18 LYS cc_start: 0.6858 (tttt) cc_final: 0.6238 (tmmt) REVERT: A 49 MET cc_start: 0.7698 (mtp) cc_final: 0.6724 (pp-130) REVERT: A 137 MET cc_start: 0.8121 (mmp) cc_final: 0.7632 (mmm) REVERT: A 147 GLU cc_start: 0.7456 (tt0) cc_final: 0.7220 (tt0) REVERT: A 213 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7948 (ttp80) REVERT: A 215 LYS cc_start: 0.7759 (tttt) cc_final: 0.7525 (tttm) REVERT: A 227 MET cc_start: 0.7000 (mmt) cc_final: 0.6173 (mtp) REVERT: A 274 LYS cc_start: 0.7509 (mttt) cc_final: 0.7236 (mttp) REVERT: A 282 ASP cc_start: 0.7710 (m-30) cc_final: 0.7475 (m-30) REVERT: A 425 ARG cc_start: 0.6549 (ttt180) cc_final: 0.6061 (ttm110) REVERT: A 433 PHE cc_start: 0.7363 (t80) cc_final: 0.7141 (t80) REVERT: O 423 TRP cc_start: 0.7958 (m100) cc_final: 0.7717 (m100) REVERT: D 14 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6454 (tt0) REVERT: D 18 LYS cc_start: 0.7016 (tttt) cc_final: 0.6359 (tmmt) REVERT: D 48 ASP cc_start: 0.7895 (m-30) cc_final: 0.7396 (m-30) REVERT: D 49 MET cc_start: 0.7754 (mtp) cc_final: 0.6878 (tmm) REVERT: D 138 MET cc_start: 0.8169 (mtt) cc_final: 0.7946 (mtt) REVERT: D 147 GLU cc_start: 0.7399 (tt0) cc_final: 0.7165 (tt0) REVERT: D 173 LYS cc_start: 0.7642 (mttm) cc_final: 0.7439 (mtpt) REVERT: D 227 MET cc_start: 0.6925 (mmt) cc_final: 0.6050 (mtp) REVERT: D 274 LYS cc_start: 0.7408 (mttt) cc_final: 0.7172 (mttp) REVERT: D 301 PHE cc_start: 0.7986 (t80) cc_final: 0.7682 (t80) REVERT: D 425 ARG cc_start: 0.6644 (ttt180) cc_final: 0.6116 (ttm110) REVERT: E 423 TRP cc_start: 0.7943 (m100) cc_final: 0.7719 (m100) REVERT: H 14 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6405 (tt0) REVERT: H 18 LYS cc_start: 0.6836 (tttt) cc_final: 0.6132 (tmmt) REVERT: H 21 LYS cc_start: 0.6448 (tttt) cc_final: 0.6140 (ttmm) REVERT: H 30 ASP cc_start: 0.8392 (m-30) cc_final: 0.8155 (m-30) REVERT: H 49 MET cc_start: 0.7734 (mtp) cc_final: 0.6807 (tmm) REVERT: H 138 MET cc_start: 0.8161 (mtt) cc_final: 0.7925 (mtt) REVERT: H 173 LYS cc_start: 0.7643 (mttm) cc_final: 0.7359 (mtpm) REVERT: H 179 GLU cc_start: 0.7772 (pm20) cc_final: 0.7554 (pm20) REVERT: H 227 MET cc_start: 0.7101 (mmt) cc_final: 0.5989 (ttp) REVERT: H 274 LYS cc_start: 0.7426 (mttt) cc_final: 0.7173 (mttp) REVERT: H 301 PHE cc_start: 0.7967 (t80) cc_final: 0.7574 (t80) REVERT: H 425 ARG cc_start: 0.6641 (ttt180) cc_final: 0.6173 (ttm110) REVERT: H 429 ILE cc_start: 0.6797 (tp) cc_final: 0.6501 (mt) REVERT: H 437 LEU cc_start: 0.7069 (mp) cc_final: 0.6766 (mp) REVERT: L 14 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6420 (tt0) REVERT: L 18 LYS cc_start: 0.6948 (tttt) cc_final: 0.6505 (mtpt) REVERT: L 30 ASP cc_start: 0.8437 (m-30) cc_final: 0.8149 (t0) REVERT: L 49 MET cc_start: 0.7811 (mtp) cc_final: 0.6828 (tmm) REVERT: L 147 GLU cc_start: 0.7528 (tt0) cc_final: 0.7254 (tt0) REVERT: L 227 MET cc_start: 0.6996 (mmt) cc_final: 0.5877 (ttp) REVERT: L 274 LYS cc_start: 0.7497 (mttt) cc_final: 0.7256 (mttp) REVERT: L 301 PHE cc_start: 0.8009 (t80) cc_final: 0.7587 (t80) REVERT: L 425 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6193 (ttm110) REVERT: Q 14 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6385 (tt0) REVERT: Q 18 LYS cc_start: 0.6858 (tttt) cc_final: 0.6198 (tmmt) REVERT: Q 48 ASP cc_start: 0.7828 (m-30) cc_final: 0.7330 (m-30) REVERT: Q 49 MET cc_start: 0.7651 (mtp) cc_final: 0.6712 (tmm) REVERT: Q 147 GLU cc_start: 0.7459 (tt0) cc_final: 0.7162 (tt0) REVERT: Q 213 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7922 (ttp80) REVERT: Q 227 MET cc_start: 0.7066 (mmt) cc_final: 0.6717 (mmp) REVERT: Q 274 LYS cc_start: 0.7437 (mttt) cc_final: 0.7209 (mttp) REVERT: Q 425 ARG cc_start: 0.6737 (ttt180) cc_final: 0.6255 (ttm110) REVERT: R 423 TRP cc_start: 0.7894 (m100) cc_final: 0.7675 (m100) outliers start: 10 outliers final: 5 residues processed: 317 average time/residue: 0.7931 time to fit residues: 280.3902 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 : 0.735 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4065 r_free = 0.4065 target = 0.190289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.140978 restraints weight = 96117.489| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.06 r_work: 0.3114 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work: 0.2924 rms_B_bonded: 3.88 restraints_weight: 0.1250 r_work (final): 0.2924 ------------------------------------------------------------------------------- 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20780 Z= 0.143 Angle : 0.655 7.653 28390 Z= 0.352 Chirality : 0.046 0.166 3185 Planarity : 0.005 0.040 3485 Dihedral : 7.591 59.955 3050 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.38 % 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 are not related in a simple way. whole: 1.38 (0.16), residues: 2505 helix: 1.69 (0.19), residues: 685 sheet: 0.89 (0.18), residues: 750 loop : 0.59 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 141 TYR 0.033 0.002 TYR L 299 PHE 0.024 0.002 PHE Q 221 TRP 0.015 0.002 TRP D 168 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (20730) covalent geometry : angle 0.63563 / 0.35 (28250) SS BOND : bond 0.00581 / 0.40 ( 10) SS BOND : angle 0.67461 / 0.44 ( 20) hydrogen bonds : bond 0.05767 / 3.75 ( 1025) hydrogen bonds : angle 5.16316 / 3.60 ( 3055) link_ALPHA1-3 : bond 0.00793 / 0.51 ( 5) link_ALPHA1-3 : angle 1.15442 / 0.85 ( 15) link_ALPHA1-6 : bond 0.00436 / 0.29 ( 5) link_ALPHA1-6 : angle 1.71009 / 1.20 ( 15) link_BETA1-4 : bond 0.00364 / 0.25 ( 15) link_BETA1-4 : angle 1.98549 / 1.31 ( 45) link_NAG-ASN : bond 0.00327 / 0.22 ( 15) link_NAG-ASN : angle 3.36195 / 2.37 ( 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 277 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 273 time to evaluate : 0.760 Fit side-chains REVERT: A 18 LYS cc_start: 0.7591 (tttt) cc_final: 0.7315 (tmmt) REVERT: A 137 MET cc_start: 0.8806 (mmp) cc_final: 0.8466 (mmm) REVERT: A 227 MET cc_start: 0.7873 (mmt) cc_final: 0.7311 (ttm) REVERT: D 18 LYS cc_start: 0.7499 (tttt) cc_final: 0.7176 (tmmt) REVERT: D 48 ASP cc_start: 0.8142 (m-30) cc_final: 0.7828 (m-30) REVERT: D 227 MET cc_start: 0.7891 (mmt) cc_final: 0.7374 (mtp) REVERT: H 18 LYS cc_start: 0.7539 (tttt) cc_final: 0.7176 (tmmt) REVERT: H 49 MET cc_start: 0.8182 (mtp) cc_final: 0.7923 (tmm) REVERT: H 227 MET cc_start: 0.7974 (mmt) cc_final: 0.7399 (ttp) REVERT: H 437 LEU cc_start: 0.7984 (mp) cc_final: 0.7738 (mp) REVERT: I 438 ILE cc_start: 0.7510 (tp) cc_final: 0.7297 (tt) REVERT: L 227 MET cc_start: 0.7967 (mmt) cc_final: 0.7402 (ttp) REVERT: Q 18 LYS cc_start: 0.7511 (tttt) cc_final: 0.7216 (tmmt) REVERT: Q 48 ASP cc_start: 0.8099 (m-30) cc_final: 0.7806 (m-30) REVERT: Q 49 MET cc_start: 0.8158 (mtp) cc_final: 0.7940 (pp-130) REVERT: Q 213 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8462 (ttm170) REVERT: Q 227 MET cc_start: 0.7884 (mmt) cc_final: 0.7327 (mtp) REVERT: R 423 TRP cc_start: 0.7898 (m100) cc_final: 0.7602 (m100) outliers start: 4 outliers final: 3 residues processed: 273 average time/residue: 0.7237 time to fit residues: 221.3308 Evaluate side-chains 255 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 252 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain M residue 483 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 53 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 217 optimal weight: 0.2980 chunk 144 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN O 461 ASN E 461 ASN H 224 GLN I 461 ASN L 224 GLN R 461 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.188132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138842 restraints weight = 100108.767| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.13 r_work: 0.3085 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work: 0.2889 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20780 Z= 0.221 Angle : 0.784 10.283 28390 Z= 0.416 Chirality : 0.051 0.231 3185 Planarity : 0.006 0.070 3485 Dihedral : 8.038 59.610 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.67 % Allowed : 5.57 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.16), residues: 2505 helix: 1.64 (0.19), residues: 685 sheet: 1.00 (0.18), residues: 775 loop : 0.70 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 28 TYR 0.036 0.004 TYR L 299 PHE 0.031 0.003 PHE Q 221 TRP 0.015 0.003 TRP A 168 HIS 0.011 0.002 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (20730) covalent geometry : angle 0.76185 / 0.41 (28250) SS BOND : bond 0.00656 / 0.45 ( 10) SS BOND : angle 1.12982 / 0.69 ( 20) hydrogen bonds : bond 0.06452 / 4.19 ( 1025) hydrogen bonds : angle 5.32360 / 3.73 ( 3055) link_ALPHA1-3 : bond 0.00697 / 0.47 ( 5) link_ALPHA1-3 : angle 1.48282 / 1.03 ( 15) link_ALPHA1-6 : bond 0.00396 / 0.26 ( 5) link_ALPHA1-6 : angle 2.66140 / 1.79 ( 15) link_BETA1-4 : bond 0.00475 / 0.32 ( 15) link_BETA1-4 : angle 2.53930 / 1.59 ( 45) link_NAG-ASN : bond 0.00591 / 0.37 ( 15) link_NAG-ASN : angle 3.69523 / 2.58 ( 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 267 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 257 time to evaluate : 0.668 Fit side-chains REVERT: A 137 MET cc_start: 0.8808 (mmp) cc_final: 0.8468 (mmm) REVERT: A 227 MET cc_start: 0.7902 (mmt) cc_final: 0.7316 (ttm) REVERT: D 18 LYS cc_start: 0.7516 (tttt) cc_final: 0.7171 (tmmt) REVERT: D 48 ASP cc_start: 0.8262 (m-30) cc_final: 0.7940 (m-30) REVERT: D 227 MET cc_start: 0.7908 (mmt) cc_final: 0.7384 (ttp) REVERT: E 470 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.5008 (mtt) REVERT: H 18 LYS cc_start: 0.7584 (tttt) cc_final: 0.7194 (tmmt) REVERT: H 49 MET cc_start: 0.8186 (mtp) cc_final: 0.7917 (pp-130) REVERT: H 227 MET cc_start: 0.8027 (mmt) cc_final: 0.7444 (ttp) REVERT: H 437 LEU cc_start: 0.8042 (mp) cc_final: 0.7809 (mp) REVERT: L 227 MET cc_start: 0.8094 (mmt) cc_final: 0.7488 (ttp) REVERT: Q 18 LYS cc_start: 0.7660 (tttt) cc_final: 0.7238 (tmmt) REVERT: Q 48 ASP cc_start: 0.8161 (m-30) cc_final: 0.7833 (m-30) REVERT: Q 49 MET cc_start: 0.8193 (mtp) cc_final: 0.7921 (pp-130) REVERT: Q 227 MET cc_start: 0.7924 (mmt) cc_final: 0.7364 (mtp) outliers start: 10 outliers final: 3 residues processed: 259 average time/residue: 0.7124 time to fit residues: 207.6906 Evaluate side-chains 257 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 253 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain M residue 483 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 37 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN D 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.191929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.142942 restraints weight = 99681.639| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 4.30 r_work: 0.3142 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work: 0.2952 rms_B_bonded: 4.16 restraints_weight: 0.1250 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20780 Z= 0.117 Angle : 0.595 8.595 28390 Z= 0.315 Chirality : 0.045 0.162 3185 Planarity : 0.004 0.038 3485 Dihedral : 6.999 56.287 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.00 % Allowed : 6.05 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 2505 helix: 2.08 (0.19), residues: 685 sheet: 1.17 (0.18), residues: 765 loop : 0.76 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 213 TYR 0.032 0.002 TYR H 299 PHE 0.018 0.002 PHE A 221 TRP 0.012 0.001 TRP I 423 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (20730) covalent geometry : angle 0.57901 / 0.31 (28250) SS BOND : bond 0.00411 / 0.28 ( 10) SS BOND : angle 0.43039 / 0.27 ( 20) hydrogen bonds : bond 0.04789 / 3.10 ( 1025) hydrogen bonds : angle 4.80170 / 3.36 ( 3055) link_ALPHA1-3 : bond 0.00558 / 0.36 ( 5) link_ALPHA1-3 : angle 1.32017 / 0.96 ( 15) link_ALPHA1-6 : bond 0.00251 / 0.16 ( 5) link_ALPHA1-6 : angle 1.58338 / 1.14 ( 15) link_BETA1-4 : bond 0.00286 / 0.20 ( 15) link_BETA1-4 : angle 1.87368 / 1.24 ( 45) link_NAG-ASN : bond 0.00259 / 0.17 ( 15) link_NAG-ASN : angle 2.78981 / 1.94 ( 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 281 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 264 time to evaluate : 0.813 Fit side-chains REVERT: A 137 MET cc_start: 0.8824 (mmp) cc_final: 0.8487 (mmm) REVERT: A 227 MET cc_start: 0.7815 (mmt) cc_final: 0.7208 (ttp) REVERT: D 18 LYS cc_start: 0.7441 (tttt) cc_final: 0.7184 (mtpt) REVERT: D 48 ASP cc_start: 0.8096 (m-30) cc_final: 0.7780 (m-30) REVERT: D 227 MET cc_start: 0.7840 (mmt) cc_final: 0.7274 (ttp) REVERT: E 470 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4874 (mtt) REVERT: H 18 LYS cc_start: 0.7497 (tttt) cc_final: 0.7109 (tmmt) REVERT: H 227 MET cc_start: 0.7944 (mmt) cc_final: 0.7330 (ttp) REVERT: H 268 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6424 (tt) REVERT: I 438 ILE cc_start: 0.7441 (tp) cc_final: 0.7239 (tt) REVERT: L 227 MET cc_start: 0.7943 (mmt) cc_final: 0.7368 (ttp) REVERT: L 268 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6345 (tt) REVERT: Q 18 LYS cc_start: 0.7474 (tttt) cc_final: 0.7109 (tmmt) REVERT: Q 48 ASP cc_start: 0.8081 (m-30) cc_final: 0.7798 (m-30) REVERT: Q 213 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8450 (mtm-85) REVERT: Q 227 MET cc_start: 0.7827 (mmt) cc_final: 0.7276 (ttm) outliers start: 17 outliers final: 5 residues processed: 270 average time/residue: 0.6950 time to fit residues: 211.6078 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 : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 272 LEU 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 268 LEU Chi-restraints excluded: chain M residue 420 ILE 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: 0.4980 chunk 202 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN L 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.191680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.143160 restraints weight = 99795.369| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 4.16 r_work: 0.3151 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work: 0.2956 rms_B_bonded: 4.00 restraints_weight: 0.1250 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20780 Z= 0.123 Angle : 0.598 7.103 28390 Z= 0.317 Chirality : 0.045 0.187 3185 Planarity : 0.004 0.037 3485 Dihedral : 6.736 54.955 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.00 % Allowed : 6.62 % Favored : 92.38 % 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 are not related in a simple way. whole: 1.86 (0.16), residues: 2505 helix: 2.14 (0.19), residues: 685 sheet: 1.14 (0.18), residues: 775 loop : 0.85 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 213 TYR 0.033 0.002 TYR H 299 PHE 0.018 0.002 PHE Q 221 TRP 0.010 0.001 TRP O 423 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (20730) covalent geometry : angle 0.58093 / 0.31 (28250) SS BOND : bond 0.00390 / 0.26 ( 10) SS BOND : angle 0.52853 / 0.33 ( 20) hydrogen bonds : bond 0.04832 / 3.13 ( 1025) hydrogen bonds : angle 4.72482 / 3.31 ( 3055) link_ALPHA1-3 : bond 0.00601 / 0.39 ( 5) link_ALPHA1-3 : angle 1.29807 / 0.94 ( 15) link_ALPHA1-6 : bond 0.00298 / 0.19 ( 5) link_ALPHA1-6 : angle 1.70480 / 1.22 ( 15) link_BETA1-4 : bond 0.00306 / 0.21 ( 15) link_BETA1-4 : angle 1.92922 / 1.26 ( 45) link_NAG-ASN : bond 0.00283 / 0.18 ( 15) link_NAG-ASN : angle 2.87236 / 2.02 ( 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: 16 poor density : 260 time to evaluate : 0.699 Fit side-chains REVERT: A 137 MET cc_start: 0.8800 (mmp) cc_final: 0.8470 (mmm) REVERT: A 227 MET cc_start: 0.7860 (mmt) cc_final: 0.7265 (ttp) REVERT: D 18 LYS cc_start: 0.7421 (tttt) cc_final: 0.7187 (mtpt) REVERT: D 48 ASP cc_start: 0.8141 (m-30) cc_final: 0.7834 (m-30) REVERT: D 227 MET cc_start: 0.7899 (mmt) cc_final: 0.7381 (mtp) REVERT: E 470 MET cc_start: 0.5406 (OUTLIER) cc_final: 0.4889 (mtt) REVERT: H 18 LYS cc_start: 0.7500 (tttt) cc_final: 0.7120 (tmmt) REVERT: H 227 MET cc_start: 0.7936 (mmt) cc_final: 0.7351 (ttp) REVERT: H 268 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6489 (tt) REVERT: L 227 MET cc_start: 0.7974 (mmt) cc_final: 0.7417 (ttp) REVERT: L 268 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6434 (tt) REVERT: Q 18 LYS cc_start: 0.7452 (tttt) cc_final: 0.7082 (tmmt) REVERT: Q 48 ASP cc_start: 0.8094 (m-30) cc_final: 0.7809 (m-30) REVERT: Q 213 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8474 (mtm-85) REVERT: Q 227 MET cc_start: 0.7856 (mmt) cc_final: 0.7578 (mmp) outliers start: 16 outliers final: 6 residues processed: 267 average time/residue: 0.6844 time to fit residues: 206.1029 Evaluate side-chains 269 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 260 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU 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 268 LEU Chi-restraints excluded: chain M residue 420 ILE 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: 0.4980 chunk 44 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 209 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 GLN M 461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.189098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.139237 restraints weight = 103490.054| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.39 r_work: 0.3099 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work: 0.2893 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20780 Z= 0.193 Angle : 0.727 8.593 28390 Z= 0.385 Chirality : 0.050 0.180 3185 Planarity : 0.005 0.059 3485 Dihedral : 7.404 56.127 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.05 % Allowed : 6.62 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.16), residues: 2505 helix: 1.81 (0.19), residues: 685 sheet: 1.16 (0.18), residues: 765 loop : 0.79 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 28 TYR 0.033 0.003 TYR L 299 PHE 0.025 0.003 PHE L 98 TRP 0.011 0.002 TRP O 423 HIS 0.009 0.002 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (20730) covalent geometry : angle 0.70621 / 0.38 (28250) SS BOND : bond 0.00574 / 0.39 ( 10) SS BOND : angle 1.14307 / 0.71 ( 20) hydrogen bonds : bond 0.05961 / 3.86 ( 1025) hydrogen bonds : angle 5.05254 / 3.55 ( 3055) link_ALPHA1-3 : bond 0.00650 / 0.43 ( 5) link_ALPHA1-3 : angle 1.41561 / 0.99 ( 15) link_ALPHA1-6 : bond 0.00269 / 0.18 ( 5) link_ALPHA1-6 : angle 2.35574 / 1.62 ( 15) link_BETA1-4 : bond 0.00434 / 0.29 ( 15) link_BETA1-4 : angle 2.36380 / 1.49 ( 45) link_NAG-ASN : bond 0.00528 / 0.34 ( 15) link_NAG-ASN : angle 3.46879 / 2.43 ( 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 280 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 0.726 Fit side-chains REVERT: A 227 MET cc_start: 0.7924 (mmt) cc_final: 0.7279 (ttp) REVERT: D 18 LYS cc_start: 0.7555 (tttt) cc_final: 0.7326 (mtpt) REVERT: D 48 ASP cc_start: 0.8190 (m-30) cc_final: 0.7864 (m-30) REVERT: D 227 MET cc_start: 0.7918 (mmt) cc_final: 0.7375 (ttp) REVERT: H 18 LYS cc_start: 0.7600 (tttt) cc_final: 0.7189 (tmmt) REVERT: H 227 MET cc_start: 0.8025 (mmt) cc_final: 0.7388 (ttp) REVERT: H 268 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6425 (tt) REVERT: L 227 MET cc_start: 0.7969 (mmt) cc_final: 0.7369 (ttp) REVERT: L 268 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6322 (tt) REVERT: M 439 SER cc_start: 0.7519 (m) cc_final: 0.7302 (t) REVERT: Q 18 LYS cc_start: 0.7654 (tttt) cc_final: 0.7239 (tmmt) REVERT: Q 48 ASP cc_start: 0.8233 (m-30) cc_final: 0.7909 (m-30) REVERT: Q 227 MET cc_start: 0.7896 (mmt) cc_final: 0.7314 (mtp) outliers start: 17 outliers final: 8 residues processed: 271 average time/residue: 0.6774 time to fit residues: 207.0381 Evaluate side-chains 270 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 260 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 H residue 272 LEU Chi-restraints excluded: chain I residue 420 ILE 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 483 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 188 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 GLN Q 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.190382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.140879 restraints weight = 107413.619| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.39 r_work: 0.3124 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work: 0.2924 rms_B_bonded: 3.97 restraints_weight: 0.1250 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20780 Z= 0.147 Angle : 0.652 7.651 28390 Z= 0.344 Chirality : 0.047 0.173 3185 Planarity : 0.005 0.043 3485 Dihedral : 7.086 54.715 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.95 % Allowed : 7.05 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.16), residues: 2505 helix: 1.92 (0.19), residues: 685 sheet: 1.18 (0.18), residues: 775 loop : 0.83 (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 D 299 PHE 0.020 0.002 PHE A 221 TRP 0.013 0.001 TRP I 423 HIS 0.005 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (20730) covalent geometry : angle 0.63392 / 0.34 (28250) SS BOND : bond 0.00432 / 0.30 ( 10) SS BOND : angle 0.79995 / 0.50 ( 20) hydrogen bonds : bond 0.05273 / 3.41 ( 1025) hydrogen bonds : angle 4.87569 / 3.43 ( 3055) link_ALPHA1-3 : bond 0.00607 / 0.40 ( 5) link_ALPHA1-3 : angle 1.34308 / 0.96 ( 15) link_ALPHA1-6 : bond 0.00239 / 0.16 ( 5) link_ALPHA1-6 : angle 1.82932 / 1.29 ( 15) link_BETA1-4 : bond 0.00345 / 0.24 ( 15) link_BETA1-4 : angle 2.11823 / 1.36 ( 45) link_NAG-ASN : bond 0.00373 / 0.24 ( 15) link_NAG-ASN : angle 3.10704 / 2.17 ( 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 275 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 0.816 Fit side-chains REVERT: A 227 MET cc_start: 0.7824 (mmt) cc_final: 0.7175 (ttp) REVERT: D 18 LYS cc_start: 0.7496 (tttt) cc_final: 0.7246 (mtpt) REVERT: D 48 ASP cc_start: 0.8172 (m-30) cc_final: 0.7840 (m-30) REVERT: D 227 MET cc_start: 0.7813 (mmt) cc_final: 0.7266 (ttp) REVERT: D 268 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6267 (tp) REVERT: H 18 LYS cc_start: 0.7566 (tttt) cc_final: 0.7179 (tmmt) REVERT: H 227 MET cc_start: 0.7955 (mmt) cc_final: 0.7327 (ttp) REVERT: H 268 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6392 (tt) REVERT: L 227 MET cc_start: 0.7895 (mmt) cc_final: 0.7329 (ttp) REVERT: L 268 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6361 (tt) REVERT: Q 18 LYS cc_start: 0.7538 (tttt) cc_final: 0.7154 (tmmt) REVERT: Q 48 ASP cc_start: 0.8133 (m-30) cc_final: 0.7812 (m-30) REVERT: Q 227 MET cc_start: 0.7846 (mmt) cc_final: 0.7263 (mtp) outliers start: 15 outliers final: 8 residues processed: 266 average time/residue: 0.6741 time to fit residues: 202.0753 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 : 0.796 ------------------------------------------------------------------------------- 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 D residue 268 LEU 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 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 483 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 217 optimal weight: 0.0030 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.0470 chunk 45 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 overall best weight: 1.9492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN B ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 GLN Q 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.189394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139697 restraints weight = 102916.382| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 4.30 r_work: 0.3106 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work: 0.2911 rms_B_bonded: 3.88 restraints_weight: 0.1250 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20780 Z= 0.177 Angle : 0.715 8.476 28390 Z= 0.376 Chirality : 0.049 0.180 3185 Planarity : 0.005 0.053 3485 Dihedral : 7.311 55.737 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.90 % Allowed : 7.05 % 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 are not related in a simple way. whole: 1.69 (0.16), residues: 2505 helix: 1.78 (0.19), residues: 685 sheet: 1.15 (0.18), residues: 775 loop : 0.80 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 28 TYR 0.033 0.003 TYR Q 157 PHE 0.023 0.002 PHE L 221 TRP 0.013 0.002 TRP I 423 HIS 0.008 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (20730) covalent geometry : angle 0.69515 / 0.37 (28250) SS BOND : bond 0.00552 / 0.38 ( 10) SS BOND : angle 1.01740 / 0.63 ( 20) hydrogen bonds : bond 0.05760 / 3.74 ( 1025) hydrogen bonds : angle 5.01373 / 3.52 ( 3055) link_ALPHA1-3 : bond 0.00630 / 0.41 ( 5) link_ALPHA1-3 : angle 1.39176 / 0.98 ( 15) link_ALPHA1-6 : bond 0.00210 / 0.14 ( 5) link_ALPHA1-6 : angle 2.18302 / 1.54 ( 15) link_BETA1-4 : bond 0.00421 / 0.29 ( 15) link_BETA1-4 : angle 2.30055 / 1.47 ( 45) link_NAG-ASN : bond 0.00515 / 0.33 ( 15) link_NAG-ASN : angle 3.35375 / 2.35 ( 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 273 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 259 time to evaluate : 0.758 Fit side-chains REVERT: A 227 MET cc_start: 0.7832 (mmt) cc_final: 0.7217 (ttp) REVERT: O 459 ARG cc_start: 0.4809 (OUTLIER) cc_final: 0.3402 (ppt170) REVERT: D 48 ASP cc_start: 0.8136 (m-30) cc_final: 0.7809 (m-30) REVERT: D 227 MET cc_start: 0.7818 (mmt) cc_final: 0.7288 (ttp) REVERT: H 18 LYS cc_start: 0.7536 (tttt) cc_final: 0.7153 (tmmt) REVERT: H 227 MET cc_start: 0.7937 (mmt) cc_final: 0.7323 (ttp) REVERT: H 268 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6442 (tt) REVERT: L 227 MET cc_start: 0.7863 (mmt) cc_final: 0.7308 (ttp) REVERT: L 268 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6364 (tt) REVERT: Q 18 LYS cc_start: 0.7597 (tttt) cc_final: 0.7187 (tmmt) REVERT: Q 227 MET cc_start: 0.7824 (mmt) cc_final: 0.7244 (mtp) outliers start: 14 outliers final: 8 residues processed: 265 average time/residue: 0.7269 time to fit residues: 216.3349 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 : 0.702 ------------------------------------------------------------------------------- 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 H residue 268 LEU Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain I residue 420 ILE 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 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: 9.9990 chunk 104 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 139 optimal weight: 0.2980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4050 r_free = 0.4050 target = 0.188856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.139234 restraints weight = 108389.275| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 4.40 r_work: 0.3102 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work: 0.2900 rms_B_bonded: 4.17 restraints_weight: 0.1250 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20780 Z= 0.201 Angle : 0.754 8.511 28390 Z= 0.397 Chirality : 0.050 0.206 3185 Planarity : 0.006 0.056 3485 Dihedral : 7.482 57.528 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.81 % Allowed : 7.29 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.16), residues: 2505 helix: 1.68 (0.19), residues: 685 sheet: 1.15 (0.18), residues: 770 loop : 0.80 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 28 TYR 0.032 0.003 TYR A 299 PHE 0.024 0.003 PHE A 221 TRP 0.015 0.002 TRP O 423 HIS 0.010 0.002 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (20730) covalent geometry : angle 0.73368 / 0.39 (28250) SS BOND : bond 0.00611 / 0.41 ( 10) SS BOND : angle 1.08478 / 0.67 ( 20) hydrogen bonds : bond 0.05989 / 3.88 ( 1025) hydrogen bonds : angle 5.09149 / 3.58 ( 3055) link_ALPHA1-3 : bond 0.00643 / 0.43 ( 5) link_ALPHA1-3 : angle 1.45366 / 1.01 ( 15) link_ALPHA1-6 : bond 0.00169 / 0.12 ( 5) link_ALPHA1-6 : angle 2.26029 / 1.57 ( 15) link_BETA1-4 : bond 0.00454 / 0.31 ( 15) link_BETA1-4 : angle 2.42293 / 1.53 ( 45) link_NAG-ASN : bond 0.00571 / 0.36 ( 15) link_NAG-ASN : angle 3.42195 / 2.39 ( 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 271 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 259 time to evaluate : 0.783 Fit side-chains REVERT: A 227 MET cc_start: 0.7827 (mmt) cc_final: 0.7214 (ttp) REVERT: O 459 ARG cc_start: 0.4857 (OUTLIER) cc_final: 0.3424 (ppt170) REVERT: D 48 ASP cc_start: 0.8160 (m-30) cc_final: 0.7826 (m-30) REVERT: D 227 MET cc_start: 0.7795 (mmt) cc_final: 0.7268 (ttp) REVERT: H 18 LYS cc_start: 0.7545 (tttt) cc_final: 0.7155 (tmmt) REVERT: H 227 MET cc_start: 0.7894 (mmt) cc_final: 0.7287 (ttp) REVERT: H 268 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6349 (tt) REVERT: L 227 MET cc_start: 0.7838 (mmt) cc_final: 0.7275 (ttp) REVERT: L 268 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6322 (tt) REVERT: Q 18 LYS cc_start: 0.7607 (tttt) cc_final: 0.7204 (tmmt) REVERT: Q 227 MET cc_start: 0.7805 (mmt) cc_final: 0.7225 (mtp) REVERT: R 459 ARG cc_start: 0.4773 (OUTLIER) cc_final: 0.3328 (ppt170) outliers start: 12 outliers final: 8 residues processed: 265 average time/residue: 0.7196 time to fit residues: 214.4847 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 : 0.710 ------------------------------------------------------------------------------- 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 H residue 268 LEU Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain I residue 420 ILE 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 483 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 217 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 167 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 GLN Q 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.192438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.143460 restraints weight = 105577.663| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 4.50 r_work: 0.3157 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work: 0.2961 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20780 Z= 0.118 Angle : 0.605 8.921 28390 Z= 0.317 Chirality : 0.045 0.163 3185 Planarity : 0.004 0.036 3485 Dihedral : 6.677 51.897 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.71 % Allowed : 7.29 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.17), residues: 2505 helix: 2.02 (0.19), residues: 685 sheet: 1.32 (0.18), residues: 765 loop : 0.87 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 213 TYR 0.032 0.002 TYR H 299 PHE 0.018 0.002 PHE L 221 TRP 0.015 0.001 TRP I 423 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (20730) covalent geometry : angle 0.59086 / 0.31 (28250) SS BOND : bond 0.00297 / 0.20 ( 10) SS BOND : angle 0.64449 / 0.41 ( 20) hydrogen bonds : bond 0.04677 / 3.02 ( 1025) hydrogen bonds : angle 4.68200 / 3.29 ( 3055) link_ALPHA1-3 : bond 0.00567 / 0.37 ( 5) link_ALPHA1-3 : angle 1.29625 / 0.95 ( 15) link_ALPHA1-6 : bond 0.00272 / 0.18 ( 5) link_ALPHA1-6 : angle 1.58253 / 1.15 ( 15) link_BETA1-4 : bond 0.00294 / 0.20 ( 15) link_BETA1-4 : angle 1.83359 / 1.21 ( 45) link_NAG-ASN : bond 0.00300 / 0.19 ( 15) link_NAG-ASN : angle 2.63256 / 1.83 ( 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 273 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 263 time to evaluate : 0.534 Fit side-chains REVERT: A 70 LYS cc_start: 0.8582 (mttp) cc_final: 0.8266 (mppt) REVERT: A 137 MET cc_start: 0.8795 (mmp) cc_final: 0.8469 (mmm) REVERT: A 227 MET cc_start: 0.7764 (mmt) cc_final: 0.7103 (ttp) REVERT: D 18 LYS cc_start: 0.7574 (mtpt) cc_final: 0.7114 (tmmt) REVERT: D 48 ASP cc_start: 0.8174 (m-30) cc_final: 0.7826 (m-30) REVERT: D 227 MET cc_start: 0.7868 (mmt) cc_final: 0.7298 (ttp) REVERT: H 18 LYS cc_start: 0.7516 (tttt) cc_final: 0.7114 (tmmt) REVERT: H 227 MET cc_start: 0.7936 (mmt) cc_final: 0.7298 (ttp) REVERT: H 268 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6335 (tt) REVERT: L 227 MET cc_start: 0.7931 (mmt) cc_final: 0.7346 (ttp) REVERT: L 268 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6307 (tt) REVERT: M 438 ILE cc_start: 0.7406 (tp) cc_final: 0.6947 (tt) REVERT: M 439 SER cc_start: 0.7454 (m) cc_final: 0.7219 (t) REVERT: Q 18 LYS cc_start: 0.7469 (tttt) cc_final: 0.7076 (tmmt) REVERT: Q 227 MET cc_start: 0.7838 (mmt) cc_final: 0.7283 (ttp) REVERT: R 459 ARG cc_start: 0.4740 (OUTLIER) cc_final: 0.4537 (pmt-80) outliers start: 10 outliers final: 5 residues processed: 268 average time/residue: 0.7167 time to fit residues: 216.2922 Evaluate side-chains 265 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU 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 L residue 268 LEU Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 459 ARG 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: 0.3980 chunk 206 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.195012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.148266 restraints weight = 106507.135| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 4.27 r_work: 0.3190 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work: 0.2998 rms_B_bonded: 4.10 restraints_weight: 0.1250 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20780 Z= 0.129 Angle : 0.630 9.607 28390 Z= 0.329 Chirality : 0.046 0.167 3185 Planarity : 0.004 0.036 3485 Dihedral : 6.608 51.584 3045 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.67 % Allowed : 7.48 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.16), residues: 2505 helix: 2.01 (0.19), residues: 685 sheet: 1.27 (0.18), residues: 775 loop : 0.85 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 213 TYR 0.033 0.002 TYR H 299 PHE 0.017 0.002 PHE Q 221 TRP 0.015 0.001 TRP I 423 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (20730) covalent geometry : angle 0.61381 / 0.33 (28250) SS BOND : bond 0.00355 / 0.24 ( 10) SS BOND : angle 0.71801 / 0.45 ( 20) hydrogen bonds : bond 0.04910 / 3.17 ( 1025) hydrogen bonds : angle 4.70071 / 3.30 ( 3055) link_ALPHA1-3 : bond 0.00601 / 0.39 ( 5) link_ALPHA1-3 : angle 1.29170 / 0.93 ( 15) link_ALPHA1-6 : bond 0.00263 / 0.18 ( 5) link_ALPHA1-6 : angle 1.66879 / 1.20 ( 15) link_BETA1-4 : bond 0.00327 / 0.22 ( 15) link_BETA1-4 : angle 1.94248 / 1.26 ( 45) link_NAG-ASN : bond 0.00323 / 0.21 ( 15) link_NAG-ASN : angle 2.88076 / 2.02 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19259.23 seconds wall clock time: 326 minutes 4.24 seconds (19564.24 seconds total)