Starting phenix.real_space_refine on Wed Jun 18 20:07:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a5v_11657/06_2025/7a5v_11657.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a5v_11657/06_2025/7a5v_11657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a5v_11657/06_2025/7a5v_11657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a5v_11657/06_2025/7a5v_11657.map" model { file = "/net/cci-nas-00/data/ceres_data/7a5v_11657/06_2025/7a5v_11657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a5v_11657/06_2025/7a5v_11657.cif" } resolution = 1.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21155 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "O" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "Q" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Conformer: "B" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} bond proxies already assigned to first conformer: 2600 Chain: "R" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 203, 281 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'NAG': 1, 'OCT': 1, 'R16': 1} Classifications: {'undetermined': 10, 'water': 193} Link IDs: {None: 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 80 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 105 residue: pdb=" N AMET A 40 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 40 " occ=0.50 residue: pdb=" N AASN A 41 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 41 " occ=0.50 residue: pdb=" N ATYR A 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 66 " occ=0.50 residue: pdb=" N AASN A 85 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 85 " occ=0.50 residue: pdb=" N ASER A 104 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 104 " occ=0.50 residue: pdb=" N ALEU A 125 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 125 " occ=0.50 residue: pdb=" N AILE A 164 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 164 " occ=0.50 residue: pdb=" N AVAL A 198 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 198 " occ=0.50 residue: pdb=" N ASER A 209 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 209 " occ=0.50 residue: pdb=" N APHE A 212 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 212 " occ=0.50 residue: pdb=" N ALEU A 214 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 214 " occ=0.50 residue: pdb=" N ATHR A 225 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 225 " occ=0.50 ... (remaining 93 not shown) Time building chain proxies: 19.92, per 1000 atoms: 0.94 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: 6.21 Conformation dependent library (CDL) restraints added in 4.6 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: 2.94 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: 10.01 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3302 1.32 - 1.45: 5963 1.45 - 1.57: 11270 1.57 - 1.70: 5 1.70 - 1.83: 190 Bond restraints: 20730 Sorted by residual: bond pdb=" N LEU A 272 " pdb=" CA LEU A 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.91e+01 bond pdb=" N LEU D 272 " pdb=" CA LEU D 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.89e+01 bond pdb=" N LEU Q 272 " pdb=" CA LEU Q 272 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.88e+01 bond pdb=" N BILE H 164 " pdb=" CA BILE H 164 " ideal model delta sigma weight residual 1.458 1.509 -0.051 1.18e-02 7.18e+03 1.88e+01 bond pdb=" N BILE L 164 " pdb=" CA BILE L 164 " ideal model delta sigma weight residual 1.458 1.508 -0.051 1.18e-02 7.18e+03 1.85e+01 ... (remaining 20725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 20431 1.71 - 3.42: 6844 3.42 - 5.14: 915 5.14 - 6.85: 50 6.85 - 8.56: 10 Bond angle restraints: 28250 Sorted by residual: angle pdb=" CA PHE H 166 " pdb=" CB PHE H 166 " pdb=" CG PHE H 166 " ideal model delta sigma weight residual 113.80 118.54 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" CA PHE A 166 " pdb=" CB PHE A 166 " pdb=" CG PHE A 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE D 166 " pdb=" CB PHE D 166 " pdb=" CG PHE D 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE Q 166 " pdb=" CB PHE Q 166 " pdb=" CG PHE Q 166 " ideal model delta sigma weight residual 113.80 118.52 -4.72 1.00e+00 1.00e+00 2.23e+01 angle pdb=" CA PHE L 166 " pdb=" CB PHE L 166 " pdb=" CG PHE L 166 " ideal model delta sigma weight residual 113.80 118.50 -4.70 1.00e+00 1.00e+00 2.21e+01 ... (remaining 28245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.01: 11940 21.01 - 42.03: 645 42.03 - 63.04: 95 63.04 - 84.06: 55 84.06 - 105.07: 25 Dihedral angle restraints: 12760 sinusoidal: 5620 harmonic: 7140 Sorted by residual: dihedral pdb=" CA SER D 46 " pdb=" C SER D 46 " pdb=" N ILE D 47 " pdb=" CA ILE D 47 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER Q 46 " pdb=" C SER Q 46 " pdb=" N ILE Q 47 " pdb=" CA ILE Q 47 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 12757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1325 0.054 - 0.109: 1148 0.109 - 0.163: 537 0.163 - 0.217: 140 0.217 - 0.272: 35 Chirality restraints: 3185 Sorted by residual: chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.33e+01 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.32e+01 chirality pdb=" C1 MAN P 4 " pdb=" O3 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.29e+01 ... (remaining 3182 not shown) Planarity restraints: 3500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.148 2.00e-02 2.50e+03 7.93e-02 1.26e+02 pdb=" CG TYR A 157 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 157 " -0.148 2.00e-02 2.50e+03 7.92e-02 1.26e+02 pdb=" CG TYR L 157 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR L 157 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR L 157 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR L 157 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR L 157 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR L 157 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR L 157 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 157 " 0.148 2.00e-02 2.50e+03 7.92e-02 1.25e+02 pdb=" CG TYR Q 157 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 157 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 157 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 157 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 157 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR Q 157 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR Q 157 " 0.119 2.00e-02 2.50e+03 ... (remaining 3497 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 10 1.96 - 2.94: 9719 2.94 - 3.92: 62588 3.92 - 4.90: 122849 Warning: very small nonbonded interaction distances. Nonbonded interactions: 195176 Sorted by model distance: nonbonded pdb="CL CL A5409 " pdb="CL CL D5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL H5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL L5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5409 " pdb="CL CL Q5409 " model vdw 0.000 3.340 nonbonded pdb="CL CL D5409 " pdb="CL CL H5409 " model vdw 0.000 3.340 ... (remaining 195171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.17 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'O' 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' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'Q' } 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 64.650 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.210 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.083 20780 Z= 0.979 Angle : 1.610 10.147 28390 Z= 1.160 Chirality : 0.089 0.272 3185 Planarity : 0.018 0.105 3485 Dihedral : 14.871 105.069 8250 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.48 % Allowed : 3.57 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.060 0.015 TRP L 168 HIS 0.034 0.008 HIS D 107 PHE 0.093 0.018 PHE H 63 TYR 0.148 0.018 TYR A 157 ARG 0.030 0.004 ARG Q 180 Details of bonding type rmsd link_NAG-ASN : bond 0.01131 ( 15) link_NAG-ASN : angle 4.55834 ( 45) link_ALPHA1-6 : bond 0.00022 ( 5) link_ALPHA1-6 : angle 4.77991 ( 15) link_BETA1-4 : bond 0.01284 ( 15) link_BETA1-4 : angle 2.99600 ( 45) link_ALPHA1-3 : bond 0.00677 ( 5) link_ALPHA1-3 : angle 2.75664 ( 15) hydrogen bonds : bond 0.17994 ( 1025) hydrogen bonds : angle 7.31449 ( 3055) SS BOND : bond 0.02364 ( 10) SS BOND : angle 2.29086 ( 20) covalent geometry : bond 0.01371 (20730) covalent geometry : angle 1.59329 (28250) *********************** 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 : 2.274 Fit side-chains REVERT: A 14 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6505 (tt0) REVERT: A 18 LYS cc_start: 0.6858 (tttt) cc_final: 0.6238 (tmmt) REVERT: A 49 MET cc_start: 0.7698 (mtp) cc_final: 0.6724 (pp-130) REVERT: A 137 MET cc_start: 0.8121 (mmp) cc_final: 0.7632 (mmm) REVERT: A 147 GLU cc_start: 0.7456 (tt0) cc_final: 0.7220 (tt0) REVERT: A 213 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7948 (ttp80) REVERT: A 215 LYS cc_start: 0.7759 (tttt) cc_final: 0.7525 (tttm) REVERT: A 227 MET cc_start: 0.7000 (mmt) cc_final: 0.6173 (mtp) REVERT: A 274 LYS cc_start: 0.7509 (mttt) cc_final: 0.7236 (mttp) REVERT: A 282 ASP cc_start: 0.7710 (m-30) cc_final: 0.7474 (m-30) REVERT: A 425 ARG cc_start: 0.6549 (ttt180) cc_final: 0.6061 (ttm110) REVERT: A 433 PHE cc_start: 0.7363 (t80) cc_final: 0.7141 (t80) REVERT: O 423 TRP cc_start: 0.7958 (m100) cc_final: 0.7717 (m100) REVERT: D 14 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6454 (tt0) REVERT: D 18 LYS cc_start: 0.7016 (tttt) cc_final: 0.6359 (tmmt) REVERT: D 48 ASP cc_start: 0.7895 (m-30) cc_final: 0.7396 (m-30) REVERT: D 49 MET cc_start: 0.7754 (mtp) cc_final: 0.6878 (tmm) REVERT: D 138 MET cc_start: 0.8169 (mtt) cc_final: 0.7946 (mtt) REVERT: D 147 GLU cc_start: 0.7399 (tt0) cc_final: 0.7165 (tt0) REVERT: D 173 LYS cc_start: 0.7642 (mttm) cc_final: 0.7439 (mtpt) REVERT: D 227 MET cc_start: 0.6925 (mmt) cc_final: 0.6050 (mtp) REVERT: D 274 LYS cc_start: 0.7408 (mttt) cc_final: 0.7172 (mttp) REVERT: D 301 PHE cc_start: 0.7986 (t80) cc_final: 0.7682 (t80) REVERT: D 425 ARG cc_start: 0.6644 (ttt180) cc_final: 0.6116 (ttm110) REVERT: E 423 TRP cc_start: 0.7943 (m100) cc_final: 0.7719 (m100) REVERT: H 14 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6405 (tt0) REVERT: H 18 LYS cc_start: 0.6836 (tttt) cc_final: 0.6132 (tmmt) REVERT: H 21 LYS cc_start: 0.6448 (tttt) cc_final: 0.6140 (ttmm) REVERT: H 30 ASP cc_start: 0.8392 (m-30) cc_final: 0.8155 (m-30) REVERT: H 49 MET cc_start: 0.7734 (mtp) cc_final: 0.6807 (tmm) REVERT: H 138 MET cc_start: 0.8161 (mtt) cc_final: 0.7925 (mtt) REVERT: H 173 LYS cc_start: 0.7643 (mttm) cc_final: 0.7359 (mtpm) REVERT: H 179 GLU cc_start: 0.7772 (pm20) cc_final: 0.7554 (pm20) REVERT: H 227 MET cc_start: 0.7101 (mmt) cc_final: 0.5989 (ttp) REVERT: H 274 LYS cc_start: 0.7426 (mttt) cc_final: 0.7173 (mttp) REVERT: H 301 PHE cc_start: 0.7967 (t80) cc_final: 0.7574 (t80) REVERT: H 425 ARG cc_start: 0.6641 (ttt180) cc_final: 0.6173 (ttm110) REVERT: H 429 ILE cc_start: 0.6797 (tp) cc_final: 0.6501 (mt) REVERT: H 437 LEU cc_start: 0.7069 (mp) cc_final: 0.6766 (mp) REVERT: L 14 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6420 (tt0) REVERT: L 18 LYS cc_start: 0.6948 (tttt) cc_final: 0.6505 (mtpt) REVERT: L 30 ASP cc_start: 0.8437 (m-30) cc_final: 0.8148 (t0) REVERT: L 49 MET cc_start: 0.7811 (mtp) cc_final: 0.6828 (tmm) REVERT: L 147 GLU cc_start: 0.7528 (tt0) cc_final: 0.7254 (tt0) REVERT: L 227 MET cc_start: 0.6996 (mmt) cc_final: 0.5877 (ttp) REVERT: L 274 LYS cc_start: 0.7497 (mttt) cc_final: 0.7256 (mttp) REVERT: L 301 PHE cc_start: 0.8009 (t80) cc_final: 0.7587 (t80) REVERT: L 425 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6193 (ttm110) REVERT: Q 14 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6385 (tt0) REVERT: Q 18 LYS cc_start: 0.6858 (tttt) cc_final: 0.6198 (tmmt) REVERT: Q 48 ASP cc_start: 0.7828 (m-30) cc_final: 0.7330 (m-30) REVERT: Q 49 MET cc_start: 0.7651 (mtp) cc_final: 0.6712 (tmm) REVERT: Q 147 GLU cc_start: 0.7459 (tt0) cc_final: 0.7162 (tt0) REVERT: Q 213 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7922 (ttp80) REVERT: Q 227 MET cc_start: 0.7066 (mmt) cc_final: 0.6717 (mmp) REVERT: Q 274 LYS cc_start: 0.7437 (mttt) cc_final: 0.7209 (mttp) REVERT: Q 425 ARG cc_start: 0.6737 (ttt180) cc_final: 0.6255 (ttm110) REVERT: R 423 TRP cc_start: 0.7894 (m100) cc_final: 0.7675 (m100) outliers start: 10 outliers final: 5 residues processed: 317 average time/residue: 1.6744 time to fit residues: 594.4991 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 : 2.027 ------------------------------------------------------------------------------- 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 189 optimal weight: 0.0470 chunk 170 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 204 optimal weight: 0.3980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN H 224 GLN L 224 GLN M 461 ASN Q 224 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.190957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.142326 restraints weight = 73590.938| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.77 r_work: 0.3112 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work: 0.2925 rms_B_bonded: 4.14 restraints_weight: 0.1250 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 20780 Z= 0.310 Angle : 1.192 18.913 28390 Z= 0.646 Chirality : 0.070 0.872 3185 Planarity : 0.016 0.382 3485 Dihedral : 12.808 128.063 3860 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.41 % Favored : 97.51 % Rotamer: Outliers : 0.67 % Allowed : 7.10 % Favored : 92.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2505 helix: -0.86 (0.18), residues: 680 sheet: 0.56 (0.18), residues: 775 loop : -0.26 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.124 0.010 TRP D 92 HIS 0.019 0.003 HIS Q 191 PHE 0.171 0.010 PHE D 433 TYR 0.143 0.008 TYR L 126 ARG 0.077 0.003 ARG E 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 15) link_NAG-ASN : angle 4.46594 ( 45) link_ALPHA1-6 : bond 0.00443 ( 5) link_ALPHA1-6 : angle 3.96163 ( 15) link_BETA1-4 : bond 0.00802 ( 15) link_BETA1-4 : angle 2.51811 ( 45) link_ALPHA1-3 : bond 0.01160 ( 5) link_ALPHA1-3 : angle 1.77650 ( 15) hydrogen bonds : bond 0.08487 ( 1025) hydrogen bonds : angle 6.23419 ( 3055) SS BOND : bond 0.00657 ( 10) SS BOND : angle 1.69848 ( 20) covalent geometry : bond 0.00629 (20730) covalent geometry : angle 1.17227 (28250) *********************** 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 296 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 283 time to evaluate : 2.225 Fit side-chains REVERT: A 137 MET cc_start: 0.8820 (mmp) cc_final: 0.8479 (mmm) REVERT: A 227 MET cc_start: 0.7980 (mmt) cc_final: 0.7500 (ttm) REVERT: D 48 ASP cc_start: 0.8245 (m-30) cc_final: 0.7922 (m-30) REVERT: D 227 MET cc_start: 0.7764 (mmt) cc_final: 0.7241 (mtp) REVERT: E 470 MET cc_start: 0.5617 (mtp) cc_final: 0.4967 (mtt) REVERT: H 18 LYS cc_start: 0.7536 (tttt) cc_final: 0.7117 (tmmt) REVERT: H 49 MET cc_start: 0.8342 (mtp) cc_final: 0.8042 (tmm) REVERT: H 227 MET cc_start: 0.7979 (mmt) cc_final: 0.7466 (ttm) REVERT: H 301 PHE cc_start: 0.8566 (t80) cc_final: 0.8255 (t80) REVERT: H 437 LEU cc_start: 0.8041 (mp) cc_final: 0.7833 (mp) REVERT: L 227 MET cc_start: 0.7906 (mmt) cc_final: 0.7424 (ttp) REVERT: M 458 SER cc_start: 0.5141 (OUTLIER) cc_final: 0.4347 (p) REVERT: Q 18 LYS cc_start: 0.7595 (tttt) cc_final: 0.7343 (tmmt) REVERT: Q 48 ASP cc_start: 0.8194 (m-30) cc_final: 0.7892 (m-30) REVERT: Q 227 MET cc_start: 0.7957 (mmt) cc_final: 0.7486 (ttp) REVERT: R 423 TRP cc_start: 0.7949 (m100) cc_final: 0.7639 (m100) outliers start: 13 outliers final: 3 residues processed: 291 average time/residue: 1.7931 time to fit residues: 585.2493 Evaluate side-chains 250 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 246 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain L residue 278 VAL Chi-restraints excluded: chain M residue 458 SER Chi-restraints excluded: chain Q residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 185 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN E 461 ASN H 90 GLN I 461 ASN L 224 GLN Q 224 GLN R 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.189151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.140256 restraints weight = 93807.029| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.04 r_work: 0.3100 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work: 0.2907 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20780 Z= 0.200 Angle : 0.771 12.468 28390 Z= 0.409 Chirality : 0.051 0.215 3185 Planarity : 0.006 0.067 3485 Dihedral : 11.353 172.302 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.71 % Allowed : 6.81 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2505 helix: 1.27 (0.19), residues: 685 sheet: 0.87 (0.18), residues: 785 loop : 0.57 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 168 HIS 0.008 0.002 HIS H 191 PHE 0.027 0.003 PHE A 221 TYR 0.037 0.003 TYR D 299 ARG 0.016 0.001 ARG L 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 15) link_NAG-ASN : angle 3.49319 ( 45) link_ALPHA1-6 : bond 0.00524 ( 5) link_ALPHA1-6 : angle 1.84186 ( 15) link_BETA1-4 : bond 0.00538 ( 15) link_BETA1-4 : angle 2.58667 ( 45) link_ALPHA1-3 : bond 0.00890 ( 5) link_ALPHA1-3 : angle 1.10305 ( 15) hydrogen bonds : bond 0.06194 ( 1025) hydrogen bonds : angle 5.37611 ( 3055) SS BOND : bond 0.00534 ( 10) SS BOND : angle 0.90371 ( 20) covalent geometry : bond 0.00418 (20730) covalent geometry : angle 0.75155 (28250) *********************** 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 274 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 262 time to evaluate : 1.913 Fit side-chains REVERT: A 137 MET cc_start: 0.8815 (mmp) cc_final: 0.8457 (mmm) REVERT: A 227 MET cc_start: 0.7907 (mmt) cc_final: 0.7338 (ttm) REVERT: D 18 LYS cc_start: 0.7564 (ttpp) cc_final: 0.7116 (ttpp) REVERT: D 48 ASP cc_start: 0.8236 (m-30) cc_final: 0.7929 (m-30) REVERT: D 227 MET cc_start: 0.7925 (mmt) cc_final: 0.7394 (ttp) REVERT: H 18 LYS cc_start: 0.7610 (tttt) cc_final: 0.7240 (tmmt) REVERT: H 49 MET cc_start: 0.8220 (mtp) cc_final: 0.7887 (tmm) REVERT: H 227 MET cc_start: 0.7988 (mmt) cc_final: 0.7431 (ttp) REVERT: I 438 ILE cc_start: 0.7536 (tp) cc_final: 0.7329 (tt) REVERT: L 227 MET cc_start: 0.8008 (mmt) cc_final: 0.7425 (ttp) REVERT: Q 18 LYS cc_start: 0.7552 (tttt) cc_final: 0.7269 (tmmt) REVERT: Q 48 ASP cc_start: 0.8089 (m-30) cc_final: 0.7780 (m-30) REVERT: Q 227 MET cc_start: 0.7917 (mmt) cc_final: 0.7359 (mtp) outliers start: 12 outliers final: 5 residues processed: 267 average time/residue: 1.5534 time to fit residues: 466.5729 Evaluate side-chains 261 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 256 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 439 SER 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 71 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN H 224 GLN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.191446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.142735 restraints weight = 100171.222| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 4.20 r_work: 0.3145 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work: 0.2946 rms_B_bonded: 4.10 restraints_weight: 0.1250 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20780 Z= 0.129 Angle : 0.627 7.597 28390 Z= 0.332 Chirality : 0.046 0.170 3185 Planarity : 0.004 0.036 3485 Dihedral : 10.253 178.581 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.67 % Allowed : 7.38 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 2505 helix: 1.97 (0.19), residues: 685 sheet: 1.05 (0.18), residues: 765 loop : 0.75 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.004 0.001 HIS Q 119 PHE 0.019 0.002 PHE Q 221 TYR 0.033 0.002 TYR D 299 ARG 0.005 0.001 ARG Q 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 15) link_NAG-ASN : angle 2.95117 ( 45) link_ALPHA1-6 : bond 0.00634 ( 5) link_ALPHA1-6 : angle 1.37449 ( 15) link_BETA1-4 : bond 0.00328 ( 15) link_BETA1-4 : angle 2.13552 ( 45) link_ALPHA1-3 : bond 0.00995 ( 5) link_ALPHA1-3 : angle 1.24456 ( 15) hydrogen bonds : bond 0.05034 ( 1025) hydrogen bonds : angle 4.91174 ( 3055) SS BOND : bond 0.00362 ( 10) SS BOND : angle 0.59543 ( 20) covalent geometry : bond 0.00254 (20730) covalent geometry : angle 0.60940 (28250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 262 time to evaluate : 2.206 Fit side-chains REVERT: A 137 MET cc_start: 0.8828 (mmp) cc_final: 0.8499 (mmm) REVERT: A 227 MET cc_start: 0.7881 (mmt) cc_final: 0.7291 (ttp) REVERT: D 18 LYS cc_start: 0.7456 (ttpp) cc_final: 0.6982 (ttpp) REVERT: D 48 ASP cc_start: 0.8149 (m-30) cc_final: 0.7846 (m-30) REVERT: D 227 MET cc_start: 0.7888 (mmt) cc_final: 0.7364 (mtp) REVERT: H 18 LYS cc_start: 0.7543 (tttt) cc_final: 0.7180 (tmmt) REVERT: H 49 MET cc_start: 0.8199 (mtp) cc_final: 0.7861 (tmm) REVERT: H 227 MET cc_start: 0.7959 (mmt) cc_final: 0.7374 (ttp) REVERT: L 227 MET cc_start: 0.7962 (mmt) cc_final: 0.7402 (ttp) REVERT: L 268 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6374 (tt) REVERT: Q 18 LYS cc_start: 0.7533 (tttt) cc_final: 0.7175 (tmmt) REVERT: Q 48 ASP cc_start: 0.8099 (m-30) cc_final: 0.7804 (m-30) REVERT: Q 213 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8468 (mtm-85) REVERT: Q 227 MET cc_start: 0.7876 (mmt) cc_final: 0.7602 (mmp) outliers start: 11 outliers final: 3 residues processed: 263 average time/residue: 1.5514 time to fit residues: 458.4389 Evaluate side-chains 263 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 259 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 483 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 154 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 chunk 172 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN O 461 ASN D 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.189903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.140019 restraints weight = 101063.726| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 4.38 r_work: 0.3108 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work: 0.2913 rms_B_bonded: 3.91 restraints_weight: 0.1250 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20780 Z= 0.161 Angle : 0.686 9.300 28390 Z= 0.363 Chirality : 0.049 0.181 3185 Planarity : 0.005 0.049 3485 Dihedral : 10.177 178.496 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.90 % Allowed : 7.33 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.16), residues: 2505 helix: 1.89 (0.19), residues: 685 sheet: 1.13 (0.18), residues: 755 loop : 0.77 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 168 HIS 0.005 0.001 HIS D 107 PHE 0.021 0.002 PHE A 221 TYR 0.033 0.003 TYR L 299 ARG 0.008 0.001 ARG Q 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 15) link_NAG-ASN : angle 3.27005 ( 45) link_ALPHA1-6 : bond 0.00711 ( 5) link_ALPHA1-6 : angle 1.56560 ( 15) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 2.33500 ( 45) link_ALPHA1-3 : bond 0.00905 ( 5) link_ALPHA1-3 : angle 1.37471 ( 15) hydrogen bonds : bond 0.05587 ( 1025) hydrogen bonds : angle 4.99852 ( 3055) SS BOND : bond 0.00485 ( 10) SS BOND : angle 0.90676 ( 20) covalent geometry : bond 0.00330 (20730) covalent geometry : angle 0.66681 (28250) *********************** 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 278 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 2.206 Fit side-chains REVERT: A 227 MET cc_start: 0.7818 (mmt) cc_final: 0.7184 (ttp) REVERT: D 18 LYS cc_start: 0.7619 (ttpp) cc_final: 0.7152 (ttpp) REVERT: D 48 ASP cc_start: 0.8052 (m-30) cc_final: 0.7723 (m-30) REVERT: D 227 MET cc_start: 0.7856 (mmt) cc_final: 0.7332 (ttp) REVERT: H 49 MET cc_start: 0.8229 (mtp) cc_final: 0.7889 (tmm) REVERT: H 227 MET cc_start: 0.7904 (mmt) cc_final: 0.7309 (ttp) REVERT: L 49 MET cc_start: 0.8321 (ptt) cc_final: 0.8011 (pp-130) REVERT: L 227 MET cc_start: 0.7886 (mmt) cc_final: 0.7315 (ttp) REVERT: Q 18 LYS cc_start: 0.7571 (tttt) cc_final: 0.7231 (tmmt) REVERT: Q 48 ASP cc_start: 0.8104 (m-30) cc_final: 0.7777 (m-30) REVERT: Q 227 MET cc_start: 0.7850 (mmt) cc_final: 0.7278 (mtp) outliers start: 15 outliers final: 6 residues processed: 270 average time/residue: 1.5619 time to fit residues: 474.4585 Evaluate side-chains 266 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 260 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain M residue 439 SER 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 120 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 180 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN Q 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.191158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.141576 restraints weight = 102484.073| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.35 r_work: 0.3131 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work: 0.2942 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20780 Z= 0.134 Angle : 0.628 7.114 28390 Z= 0.331 Chirality : 0.047 0.185 3185 Planarity : 0.004 0.035 3485 Dihedral : 9.619 179.260 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.90 % Allowed : 7.67 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.16), residues: 2505 helix: 2.01 (0.19), residues: 685 sheet: 1.07 (0.18), residues: 775 loop : 0.89 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 423 HIS 0.003 0.001 HIS D 107 PHE 0.019 0.002 PHE Q 221 TYR 0.033 0.002 TYR D 299 ARG 0.007 0.001 ARG H 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 15) link_NAG-ASN : angle 2.99698 ( 45) link_ALPHA1-6 : bond 0.00809 ( 5) link_ALPHA1-6 : angle 1.30841 ( 15) link_BETA1-4 : bond 0.00349 ( 15) link_BETA1-4 : angle 2.09681 ( 45) link_ALPHA1-3 : bond 0.00982 ( 5) link_ALPHA1-3 : angle 1.38325 ( 15) hydrogen bonds : bond 0.05041 ( 1025) hydrogen bonds : angle 4.79922 ( 3055) SS BOND : bond 0.00370 ( 10) SS BOND : angle 0.69862 ( 20) covalent geometry : bond 0.00269 (20730) covalent geometry : angle 0.61102 (28250) *********************** 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 276 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 2.106 Fit side-chains REVERT: A 227 MET cc_start: 0.7764 (mmt) cc_final: 0.7118 (ttp) REVERT: D 18 LYS cc_start: 0.7546 (ttpp) cc_final: 0.7076 (ttpp) REVERT: D 48 ASP cc_start: 0.8032 (m-30) cc_final: 0.7705 (m-30) REVERT: D 227 MET cc_start: 0.7840 (mmt) cc_final: 0.7300 (ttp) REVERT: D 425 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7270 (mtm-85) REVERT: H 18 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7136 (tmmt) REVERT: H 49 MET cc_start: 0.8162 (mtp) cc_final: 0.7927 (pp-130) REVERT: H 227 MET cc_start: 0.7881 (mmt) cc_final: 0.7297 (ttp) REVERT: H 268 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6391 (tt) REVERT: L 49 MET cc_start: 0.8275 (ptt) cc_final: 0.8025 (pp-130) REVERT: L 227 MET cc_start: 0.7858 (mmt) cc_final: 0.7303 (ttp) REVERT: Q 18 LYS cc_start: 0.7535 (tttt) cc_final: 0.7134 (tmmt) REVERT: Q 213 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8480 (mtm-85) REVERT: Q 227 MET cc_start: 0.7824 (mmt) cc_final: 0.7532 (mmp) outliers start: 15 outliers final: 9 residues processed: 269 average time/residue: 2.0778 time to fit residues: 634.4578 Evaluate side-chains 269 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 259 time to evaluate : 4.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 439 SER 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 210 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 217 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.4058 r_free = 0.4058 target = 0.189579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139710 restraints weight = 105842.985| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.35 r_work: 0.3106 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work: 0.2901 rms_B_bonded: 3.96 restraints_weight: 0.1250 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-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: 9 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20780 Z= 0.171 Angle : 0.704 9.915 28390 Z= 0.370 Chirality : 0.049 0.201 3185 Planarity : 0.005 0.049 3485 Dihedral : 9.735 178.438 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.95 % Allowed : 7.86 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.16), residues: 2505 helix: 1.84 (0.19), residues: 685 sheet: 1.12 (0.18), residues: 765 loop : 0.85 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 423 HIS 0.006 0.001 HIS D 107 PHE 0.022 0.002 PHE A 221 TYR 0.033 0.003 TYR L 299 ARG 0.008 0.001 ARG Q 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 15) link_NAG-ASN : angle 3.31844 ( 45) link_ALPHA1-6 : bond 0.00857 ( 5) link_ALPHA1-6 : angle 1.42069 ( 15) link_BETA1-4 : bond 0.00425 ( 15) link_BETA1-4 : angle 2.33043 ( 45) link_ALPHA1-3 : bond 0.00951 ( 5) link_ALPHA1-3 : angle 1.47767 ( 15) hydrogen bonds : bond 0.05665 ( 1025) hydrogen bonds : angle 4.97646 ( 3055) SS BOND : bond 0.00484 ( 10) SS BOND : angle 1.05370 ( 20) covalent geometry : bond 0.00356 (20730) covalent geometry : angle 0.68425 (28250) *********************** 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 276 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 2.190 Fit side-chains REVERT: A 227 MET cc_start: 0.7880 (mmt) cc_final: 0.7242 (ttm) REVERT: D 18 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7113 (ttpp) REVERT: D 48 ASP cc_start: 0.8067 (m-30) cc_final: 0.7722 (m-30) REVERT: D 227 MET cc_start: 0.7893 (mmt) cc_final: 0.7334 (ttp) REVERT: H 18 LYS cc_start: 0.7575 (mtpt) cc_final: 0.7092 (tmmt) REVERT: H 49 MET cc_start: 0.8239 (mtp) cc_final: 0.7921 (pp-130) REVERT: H 227 MET cc_start: 0.7964 (mmt) cc_final: 0.7347 (ttp) REVERT: H 268 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6371 (tt) REVERT: L 49 MET cc_start: 0.8386 (ptt) cc_final: 0.8083 (pp-130) REVERT: L 227 MET cc_start: 0.7898 (mmt) cc_final: 0.7331 (ttp) REVERT: Q 18 LYS cc_start: 0.7608 (tttt) cc_final: 0.7187 (tmmt) REVERT: Q 227 MET cc_start: 0.7887 (mmt) cc_final: 0.7294 (mtp) outliers start: 15 outliers final: 12 residues processed: 269 average time/residue: 1.6683 time to fit residues: 506.2091 Evaluate side-chains 274 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 261 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 470 MET Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 470 MET Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 70 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 95 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN B H 224 GLN M 461 ASN Q 224 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.189298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.139914 restraints weight = 104506.767| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.35 r_work: 0.3104 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work: 0.2899 rms_B_bonded: 4.03 restraints_weight: 0.1250 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20780 Z= 0.180 Angle : 0.713 8.472 28390 Z= 0.376 Chirality : 0.050 0.211 3185 Planarity : 0.005 0.051 3485 Dihedral : 9.822 178.225 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.90 % Allowed : 8.14 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.16), residues: 2505 helix: 1.76 (0.19), residues: 685 sheet: 1.08 (0.18), residues: 775 loop : 0.86 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 423 HIS 0.007 0.001 HIS D 107 PHE 0.021 0.002 PHE A 221 TYR 0.032 0.003 TYR Q 157 ARG 0.008 0.001 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 15) link_NAG-ASN : angle 3.36247 ( 45) link_ALPHA1-6 : bond 0.00864 ( 5) link_ALPHA1-6 : angle 1.40445 ( 15) link_BETA1-4 : bond 0.00445 ( 15) link_BETA1-4 : angle 2.33510 ( 45) link_ALPHA1-3 : bond 0.00980 ( 5) link_ALPHA1-3 : angle 1.39691 ( 15) hydrogen bonds : bond 0.05734 ( 1025) hydrogen bonds : angle 5.00687 ( 3055) SS BOND : bond 0.00539 ( 10) SS BOND : angle 1.00519 ( 20) covalent geometry : bond 0.00375 (20730) covalent geometry : angle 0.69369 (28250) *********************** 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 276 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 2.151 Fit side-chains REVERT: A 227 MET cc_start: 0.7935 (mmt) cc_final: 0.7271 (ttp) REVERT: D 18 LYS cc_start: 0.7642 (ttpp) cc_final: 0.7165 (ttpp) REVERT: D 48 ASP cc_start: 0.8191 (m-30) cc_final: 0.7832 (m-30) REVERT: D 49 MET cc_start: 0.8145 (pmt) cc_final: 0.7820 (pp-130) REVERT: D 227 MET cc_start: 0.7899 (mmt) cc_final: 0.7345 (ttp) REVERT: H 18 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7162 (tmmt) REVERT: H 49 MET cc_start: 0.8255 (mtp) cc_final: 0.7951 (pp-130) REVERT: H 227 MET cc_start: 0.7982 (mmt) cc_final: 0.7363 (ttp) REVERT: H 268 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6335 (tt) REVERT: L 49 MET cc_start: 0.8446 (ptt) cc_final: 0.8190 (pp-130) REVERT: L 227 MET cc_start: 0.7918 (mmt) cc_final: 0.7346 (ttp) REVERT: Q 18 LYS cc_start: 0.7634 (tttt) cc_final: 0.7225 (tmmt) REVERT: Q 227 MET cc_start: 0.7900 (mmt) cc_final: 0.7312 (mtp) outliers start: 14 outliers final: 12 residues processed: 268 average time/residue: 1.5401 time to fit residues: 464.6164 Evaluate side-chains 273 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 2.143 ------------------------------------------------------------------------------- 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 E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 470 MET Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 470 MET Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 156 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.191108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.142032 restraints weight = 101483.695| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.19 r_work: 0.3132 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work: 0.2947 rms_B_bonded: 3.90 restraints_weight: 0.1250 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20780 Z= 0.134 Angle : 0.638 8.456 28390 Z= 0.334 Chirality : 0.047 0.217 3185 Planarity : 0.004 0.034 3485 Dihedral : 9.318 179.329 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.95 % Allowed : 7.95 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.16), residues: 2505 helix: 1.93 (0.19), residues: 685 sheet: 1.17 (0.18), residues: 775 loop : 0.89 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 423 HIS 0.004 0.001 HIS H 191 PHE 0.018 0.002 PHE Q 221 TYR 0.033 0.002 TYR D 299 ARG 0.005 0.001 ARG L 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 15) link_NAG-ASN : angle 2.97142 ( 45) link_ALPHA1-6 : bond 0.00949 ( 5) link_ALPHA1-6 : angle 1.19370 ( 15) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 2.01002 ( 45) link_ALPHA1-3 : bond 0.01046 ( 5) link_ALPHA1-3 : angle 1.34910 ( 15) hydrogen bonds : bond 0.05037 ( 1025) hydrogen bonds : angle 4.78051 ( 3055) SS BOND : bond 0.00345 ( 10) SS BOND : angle 0.78676 ( 20) covalent geometry : bond 0.00271 (20730) covalent geometry : angle 0.62127 (28250) *********************** 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 275 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 1.925 Fit side-chains REVERT: A 227 MET cc_start: 0.7804 (mmt) cc_final: 0.7168 (ttp) REVERT: D 18 LYS cc_start: 0.7588 (ttpp) cc_final: 0.7066 (ttpp) REVERT: D 48 ASP cc_start: 0.8088 (m-30) cc_final: 0.7726 (m-30) REVERT: D 227 MET cc_start: 0.7846 (mmt) cc_final: 0.7310 (ttp) REVERT: D 425 ARG cc_start: 0.7522 (ttm110) cc_final: 0.7308 (mtm-85) REVERT: H 18 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7171 (tmmt) REVERT: H 49 MET cc_start: 0.8190 (mtp) cc_final: 0.7955 (pp-130) REVERT: H 227 MET cc_start: 0.7921 (mmt) cc_final: 0.7342 (ttp) REVERT: H 268 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6437 (tt) REVERT: L 227 MET cc_start: 0.7872 (mmt) cc_final: 0.7335 (ttp) REVERT: Q 18 LYS cc_start: 0.7568 (tttt) cc_final: 0.7195 (tmmt) REVERT: Q 213 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8491 (mtm-85) REVERT: Q 227 MET cc_start: 0.7826 (mmt) cc_final: 0.7540 (mmp) outliers start: 15 outliers final: 12 residues processed: 268 average time/residue: 1.4989 time to fit residues: 451.8918 Evaluate side-chains 273 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 2.239 ------------------------------------------------------------------------------- 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 E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 456 THR Chi-restraints excluded: chain R residue 470 MET Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 171 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.189532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.139600 restraints weight = 106462.597| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.34 r_work: 0.3109 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work: 0.2905 rms_B_bonded: 3.85 restraints_weight: 0.1250 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20780 Z= 0.190 Angle : 0.749 11.841 28390 Z= 0.391 Chirality : 0.051 0.232 3185 Planarity : 0.005 0.053 3485 Dihedral : 9.624 178.301 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.86 % Allowed : 8.14 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.16), residues: 2505 helix: 1.70 (0.19), residues: 685 sheet: 1.13 (0.18), residues: 775 loop : 0.85 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 423 HIS 0.006 0.002 HIS D 107 PHE 0.024 0.002 PHE L 98 TYR 0.033 0.003 TYR L 299 ARG 0.009 0.001 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 15) link_NAG-ASN : angle 3.37991 ( 45) link_ALPHA1-6 : bond 0.00900 ( 5) link_ALPHA1-6 : angle 1.45436 ( 15) link_BETA1-4 : bond 0.00483 ( 15) link_BETA1-4 : angle 2.38462 ( 45) link_ALPHA1-3 : bond 0.01003 ( 5) link_ALPHA1-3 : angle 1.43877 ( 15) hydrogen bonds : bond 0.05856 ( 1025) hydrogen bonds : angle 5.02859 ( 3055) SS BOND : bond 0.00546 ( 10) SS BOND : angle 1.14773 ( 20) covalent geometry : bond 0.00401 (20730) covalent geometry : angle 0.73026 (28250) ********************** 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 274 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 261 time to evaluate : 2.185 Fit side-chains REVERT: A 227 MET cc_start: 0.7885 (mmt) cc_final: 0.7232 (ttp) REVERT: D 18 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7154 (ttpp) REVERT: D 48 ASP cc_start: 0.7968 (m-30) cc_final: 0.7609 (m-30) REVERT: D 227 MET cc_start: 0.7895 (mmt) cc_final: 0.7352 (ttp) REVERT: H 18 LYS cc_start: 0.7625 (mtpt) cc_final: 0.7170 (tmmt) REVERT: H 49 MET cc_start: 0.8224 (mtp) cc_final: 0.7937 (pp-130) REVERT: H 227 MET cc_start: 0.7963 (mmt) cc_final: 0.7354 (ttp) REVERT: H 268 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6482 (tt) REVERT: L 227 MET cc_start: 0.7932 (mmt) cc_final: 0.7357 (ttp) REVERT: Q 18 LYS cc_start: 0.7611 (tttt) cc_final: 0.7246 (tmmt) REVERT: Q 227 MET cc_start: 0.7891 (mmt) cc_final: 0.7314 (mtp) outliers start: 13 outliers final: 12 residues processed: 267 average time/residue: 1.4989 time to fit residues: 450.0892 Evaluate side-chains 273 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 1.902 ------------------------------------------------------------------------------- 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 E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 439 SER Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 456 THR Chi-restraints excluded: chain R residue 470 MET Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 39 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 176 optimal weight: 30.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN B Q 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.191557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.142132 restraints weight = 102877.282| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 4.36 r_work: 0.3138 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work: 0.2943 rms_B_bonded: 4.04 restraints_weight: 0.1250 r_work (final): 0.2943 ------------------------------------------------------------------------------- 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: 25 | |-----------------------------------------------------------------------------| |-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: 25 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20780 Z= 0.132 Angle : 0.637 8.588 28390 Z= 0.333 Chirality : 0.047 0.226 3185 Planarity : 0.004 0.038 3485 Dihedral : 9.145 179.414 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.95 % Allowed : 8.10 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.16), residues: 2505 helix: 1.88 (0.19), residues: 685 sheet: 1.26 (0.18), residues: 765 loop : 0.88 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 423 HIS 0.004 0.001 HIS H 191 PHE 0.018 0.002 PHE Q 221 TYR 0.033 0.002 TYR D 299 ARG 0.007 0.001 ARG L 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 15) link_NAG-ASN : angle 2.93004 ( 45) link_ALPHA1-6 : bond 0.00959 ( 5) link_ALPHA1-6 : angle 1.17738 ( 15) link_BETA1-4 : bond 0.00341 ( 15) link_BETA1-4 : angle 1.96558 ( 45) link_ALPHA1-3 : bond 0.01045 ( 5) link_ALPHA1-3 : angle 1.31834 ( 15) hydrogen bonds : bond 0.04963 ( 1025) hydrogen bonds : angle 4.76844 ( 3055) SS BOND : bond 0.00326 ( 10) SS BOND : angle 0.79292 ( 20) covalent geometry : bond 0.00267 (20730) covalent geometry : angle 0.62122 (28250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41168.13 seconds wall clock time: 711 minutes 20.04 seconds (42680.04 seconds total)