Starting phenix.real_space_refine on Sun Sep 29 06:25:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/09_2024/7a5v_11657.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/09_2024/7a5v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/09_2024/7a5v_11657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/09_2024/7a5v_11657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/09_2024/7a5v_11657.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5v_11657/09_2024/7a5v_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 19.24, per 1000 atoms: 0.91 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: 5.39 Conformation dependent library (CDL) restraints added in 3.7 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: 2.47 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: 7.73 Time building geometry restraints manager: 6.13 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) selection = (chain 'D' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) selection = (chain 'H' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) selection = (chain 'L' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) selection = (chain 'Q' and (resid 7 through 39 or resid 42 through 43 or resid 45 through 52 \ or resid 54 through 63 or resid 65 or resid 67 through 84 or resid 86 through 1 \ 03 or resid 105 through 111 or resid 113 through 124 or resid 126 through 135 or \ resid 137 through 149 or resid 151 through 163 or resid 165 through 197 or resi \ d 199 through 208 or resid 210 through 211 or resid 213 or resid 215 through 224 \ or resid 226 through 228 or resid 230 through 240 or resid 244 through 278 or r \ esid 280 through 425 or resid 427 through 433 or resid 435 through 447 or resid \ 5401 through 5410)) } 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 'E' selection = chain 'I' selection = chain 'M' selection = chain 'O' selection = chain 'R' } 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: 5.750 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: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 55.470 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 74.020 ------------------------------------------------------------------------------- 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 20730 Z= 0.880 Angle : 1.593 8.558 28250 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 307 time to evaluate : 2.142 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: 1.5747 time to fit residues: 555.9110 Evaluate side-chains 270 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 265 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 20730 Z= 0.391 Angle : 1.154 22.808 28250 Z= 0.627 Chirality : 0.068 0.755 3185 Planarity : 0.015 0.394 3485 Dihedral : 12.786 142.344 3860 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.49 % Favored : 97.37 % Rotamer: Outliers : 0.81 % Allowed : 7.43 % Favored : 91.76 % 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: -0.53 (0.16), residues: 2505 helix: -0.95 (0.18), residues: 680 sheet: 0.44 (0.18), residues: 775 loop : -0.37 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.010 TRP I 440 HIS 0.020 0.004 HIS Q 191 PHE 0.175 0.009 PHE D 433 TYR 0.138 0.008 TYR L 126 ARG 0.081 0.003 ARG E 459 *********************** 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 299 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 283 time to evaluate : 2.125 Fit side-chains REVERT: A 14 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6355 (tt0) REVERT: A 18 LYS cc_start: 0.6844 (tttt) cc_final: 0.6429 (mtpt) REVERT: A 49 MET cc_start: 0.7553 (mtp) cc_final: 0.6703 (pp-130) REVERT: A 137 MET cc_start: 0.8066 (mmp) cc_final: 0.7623 (mmm) REVERT: A 147 GLU cc_start: 0.7362 (tt0) cc_final: 0.7140 (tt0) REVERT: A 215 LYS cc_start: 0.7654 (tttt) cc_final: 0.7426 (tttm) REVERT: A 227 MET cc_start: 0.6943 (mmt) cc_final: 0.5911 (ttm) REVERT: A 274 LYS cc_start: 0.7479 (mttt) cc_final: 0.7209 (mttp) REVERT: A 425 ARG cc_start: 0.6486 (ttt180) cc_final: 0.6037 (ttm110) REVERT: O 423 TRP cc_start: 0.7786 (m100) cc_final: 0.7558 (m100) REVERT: D 14 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6342 (tt0) REVERT: D 18 LYS cc_start: 0.6840 (tttt) cc_final: 0.6272 (pptt) REVERT: D 21 LYS cc_start: 0.6428 (tttm) cc_final: 0.6008 (tppt) REVERT: D 48 ASP cc_start: 0.7793 (m-30) cc_final: 0.7291 (m-30) REVERT: D 49 MET cc_start: 0.7615 (mtp) cc_final: 0.6720 (tmm) REVERT: D 147 GLU cc_start: 0.7296 (tt0) cc_final: 0.7073 (tt0) REVERT: D 173 LYS cc_start: 0.7565 (mttm) cc_final: 0.7250 (mmmt) REVERT: D 227 MET cc_start: 0.6714 (mmt) cc_final: 0.5830 (mtp) REVERT: D 274 LYS cc_start: 0.7364 (mttt) cc_final: 0.7106 (mttp) REVERT: D 301 PHE cc_start: 0.7652 (t80) cc_final: 0.7402 (t80) REVERT: D 425 ARG cc_start: 0.6593 (ttt180) cc_final: 0.6090 (ttm110) REVERT: E 423 TRP cc_start: 0.7786 (m100) cc_final: 0.7557 (m100) REVERT: E 470 MET cc_start: 0.5467 (mtp) cc_final: 0.4741 (mtt) REVERT: H 14 GLU cc_start: 0.6414 (mt-10) cc_final: 0.6138 (tt0) REVERT: H 18 LYS cc_start: 0.6760 (tttt) cc_final: 0.6031 (tmmt) REVERT: H 30 ASP cc_start: 0.7861 (m-30) cc_final: 0.7637 (m-30) REVERT: H 49 MET cc_start: 0.7653 (mtp) cc_final: 0.6674 (tmm) REVERT: H 173 LYS cc_start: 0.7571 (mttm) cc_final: 0.7315 (mtpm) REVERT: H 227 MET cc_start: 0.7103 (mmt) cc_final: 0.6062 (ttm) REVERT: H 274 LYS cc_start: 0.7390 (mttt) cc_final: 0.7105 (mttp) REVERT: H 301 PHE cc_start: 0.7791 (t80) cc_final: 0.7378 (t80) REVERT: H 425 ARG cc_start: 0.6530 (ttt180) cc_final: 0.6138 (ttm170) REVERT: H 429 ILE cc_start: 0.6574 (tp) cc_final: 0.6258 (mm) REVERT: H 437 LEU cc_start: 0.7039 (mp) cc_final: 0.6762 (mp) REVERT: L 14 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6370 (tt0) REVERT: L 18 LYS cc_start: 0.6818 (tttt) cc_final: 0.6520 (ttmt) REVERT: L 49 MET cc_start: 0.7464 (mtp) cc_final: 0.6725 (tmm) REVERT: L 147 GLU cc_start: 0.7381 (tt0) cc_final: 0.7125 (tt0) REVERT: L 227 MET cc_start: 0.7001 (mmt) cc_final: 0.5990 (ttp) REVERT: L 301 PHE cc_start: 0.7882 (t80) cc_final: 0.7466 (t80) REVERT: L 425 ARG cc_start: 0.6586 (ttt180) cc_final: 0.6105 (ttm110) REVERT: M 458 SER cc_start: 0.5029 (OUTLIER) cc_final: 0.4215 (p) REVERT: M 459 ARG cc_start: 0.4533 (OUTLIER) cc_final: 0.4319 (ppt90) REVERT: M 471 ASN cc_start: 0.3517 (OUTLIER) cc_final: 0.3195 (p0) REVERT: Q 14 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6173 (tt0) REVERT: Q 18 LYS cc_start: 0.6823 (tttt) cc_final: 0.6184 (tmmt) REVERT: Q 48 ASP cc_start: 0.7723 (m-30) cc_final: 0.7255 (m-30) REVERT: Q 49 MET cc_start: 0.7606 (mtp) cc_final: 0.6692 (pp-130) REVERT: Q 147 GLU cc_start: 0.7375 (tt0) cc_final: 0.7116 (tt0) REVERT: Q 213 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7849 (ttp80) REVERT: Q 227 MET cc_start: 0.6990 (mmt) cc_final: 0.6136 (ttp) REVERT: Q 274 LYS cc_start: 0.7347 (mttt) cc_final: 0.7143 (mttp) REVERT: Q 425 ARG cc_start: 0.6510 (ttt180) cc_final: 0.6066 (ttm110) REVERT: R 423 TRP cc_start: 0.7771 (m100) cc_final: 0.7358 (m100) outliers start: 16 outliers final: 4 residues processed: 292 average time/residue: 1.4500 time to fit residues: 475.7249 Evaluate side-chains 269 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 262 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 M residue 459 ARG Chi-restraints excluded: chain M residue 471 ASN Chi-restraints excluded: chain M residue 483 CYS 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 113 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 204 optimal weight: 7.9990 chunk 221 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 202 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 224 GLN E 461 ASN L 224 GLN Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20730 Z= 0.185 Angle : 0.641 6.371 28250 Z= 0.348 Chirality : 0.047 0.169 3185 Planarity : 0.005 0.041 3485 Dihedral : 10.391 78.059 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.48 % Allowed : 7.33 % Favored : 92.19 % 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: 1.15 (0.16), residues: 2505 helix: 1.31 (0.19), residues: 685 sheet: 0.89 (0.18), residues: 760 loop : 0.45 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 92 HIS 0.005 0.001 HIS D 107 PHE 0.022 0.002 PHE Q 105 TYR 0.031 0.002 TYR D 299 ARG 0.014 0.001 ARG M 459 *********************** 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 280 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 271 time to evaluate : 2.030 Fit side-chains REVERT: A 14 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6318 (tt0) REVERT: A 18 LYS cc_start: 0.6843 (tttt) cc_final: 0.6421 (mtpt) REVERT: A 49 MET cc_start: 0.7467 (mtp) cc_final: 0.6643 (pp-130) REVERT: A 137 MET cc_start: 0.8071 (mmp) cc_final: 0.7577 (mmm) REVERT: A 227 MET cc_start: 0.6927 (mmt) cc_final: 0.5839 (ttm) REVERT: A 274 LYS cc_start: 0.7521 (mttt) cc_final: 0.7282 (mttp) REVERT: A 425 ARG cc_start: 0.6496 (ttt180) cc_final: 0.6076 (ttm110) REVERT: D 14 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6395 (tt0) REVERT: D 18 LYS cc_start: 0.6798 (tttt) cc_final: 0.6455 (ttpp) REVERT: D 21 LYS cc_start: 0.6541 (tttm) cc_final: 0.6042 (tppt) REVERT: D 48 ASP cc_start: 0.7775 (m-30) cc_final: 0.7280 (m-30) REVERT: D 49 MET cc_start: 0.7465 (mtp) cc_final: 0.6656 (tmm) REVERT: D 147 GLU cc_start: 0.7285 (tt0) cc_final: 0.7044 (tt0) REVERT: D 173 LYS cc_start: 0.7613 (mttm) cc_final: 0.7283 (mmtt) REVERT: D 227 MET cc_start: 0.7002 (mmt) cc_final: 0.6150 (mtp) REVERT: D 274 LYS cc_start: 0.7274 (mttt) cc_final: 0.6977 (mttp) REVERT: D 301 PHE cc_start: 0.7773 (t80) cc_final: 0.7507 (t80) REVERT: D 425 ARG cc_start: 0.6520 (ttt180) cc_final: 0.6039 (ttm110) REVERT: E 423 TRP cc_start: 0.7774 (m100) cc_final: 0.7538 (m100) REVERT: E 470 MET cc_start: 0.5505 (mtp) cc_final: 0.4786 (mtt) REVERT: H 14 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6256 (tt0) REVERT: H 18 LYS cc_start: 0.6729 (tttt) cc_final: 0.6296 (mtpt) REVERT: H 30 ASP cc_start: 0.8247 (m-30) cc_final: 0.8008 (m-30) REVERT: H 49 MET cc_start: 0.7543 (mtp) cc_final: 0.6566 (tmm) REVERT: H 103 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7592 (tptp) REVERT: H 173 LYS cc_start: 0.7609 (mttm) cc_final: 0.7337 (mtpm) REVERT: H 227 MET cc_start: 0.7075 (mmt) cc_final: 0.5984 (ttp) REVERT: H 274 LYS cc_start: 0.7369 (mttt) cc_final: 0.7155 (mttp) REVERT: H 301 PHE cc_start: 0.7775 (t80) cc_final: 0.7304 (t80) REVERT: H 425 ARG cc_start: 0.6407 (ttt180) cc_final: 0.6005 (ttm110) REVERT: H 437 LEU cc_start: 0.6979 (mp) cc_final: 0.6736 (mp) REVERT: L 14 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6346 (tt0) REVERT: L 49 MET cc_start: 0.7542 (mtp) cc_final: 0.6766 (tmm) REVERT: L 147 GLU cc_start: 0.7393 (tt0) cc_final: 0.7144 (tt0) REVERT: L 227 MET cc_start: 0.7016 (mmt) cc_final: 0.5966 (ttp) REVERT: L 425 ARG cc_start: 0.6542 (ttt180) cc_final: 0.6108 (ttm110) REVERT: Q 14 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6249 (tt0) REVERT: Q 18 LYS cc_start: 0.6789 (tttt) cc_final: 0.6141 (tmmt) REVERT: Q 48 ASP cc_start: 0.7660 (m-30) cc_final: 0.7210 (m-30) REVERT: Q 49 MET cc_start: 0.7403 (mtp) cc_final: 0.6529 (pp-130) REVERT: Q 147 GLU cc_start: 0.7341 (tt0) cc_final: 0.7001 (tt0) REVERT: Q 213 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7853 (ttp80) REVERT: Q 227 MET cc_start: 0.6944 (mmt) cc_final: 0.6574 (mmp) REVERT: Q 274 LYS cc_start: 0.7397 (mttt) cc_final: 0.7186 (mttp) REVERT: Q 425 ARG cc_start: 0.6565 (ttt180) cc_final: 0.6098 (ttm110) REVERT: R 423 TRP cc_start: 0.7751 (m100) cc_final: 0.7550 (m100) outliers start: 9 outliers final: 3 residues processed: 274 average time/residue: 1.5050 time to fit residues: 461.3342 Evaluate side-chains 266 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 262 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 439 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 137 optimal weight: 0.0670 chunk 205 optimal weight: 0.9980 chunk 217 optimal weight: 0.0370 chunk 107 optimal weight: 0.0980 chunk 194 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20730 Z= 0.132 Angle : 0.539 6.220 28250 Z= 0.290 Chirality : 0.044 0.193 3185 Planarity : 0.004 0.037 3485 Dihedral : 8.913 68.455 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.29 % Allowed : 7.71 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.80 (0.17), residues: 2505 helix: 2.20 (0.19), residues: 680 sheet: 1.16 (0.18), residues: 765 loop : 0.69 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 168 HIS 0.003 0.001 HIS Q 191 PHE 0.016 0.001 PHE Q 221 TYR 0.028 0.001 TYR A 299 ARG 0.007 0.000 ARG L 141 *********************** 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 270 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 265 time to evaluate : 2.077 Fit side-chains REVERT: A 14 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6233 (tt0) REVERT: A 18 LYS cc_start: 0.6773 (tttt) cc_final: 0.6293 (mtmm) REVERT: A 49 MET cc_start: 0.7382 (mtp) cc_final: 0.6657 (pp-130) REVERT: A 137 MET cc_start: 0.8005 (mmp) cc_final: 0.7526 (mmm) REVERT: A 227 MET cc_start: 0.6831 (mmt) cc_final: 0.5700 (ttp) REVERT: A 425 ARG cc_start: 0.6435 (ttt180) cc_final: 0.6018 (ttm110) REVERT: O 438 ILE cc_start: 0.6995 (tt) cc_final: 0.6789 (tp) REVERT: D 14 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6369 (tt0) REVERT: D 18 LYS cc_start: 0.6677 (tttt) cc_final: 0.6127 (mtmm) REVERT: D 21 LYS cc_start: 0.6486 (tttm) cc_final: 0.6023 (tppt) REVERT: D 48 ASP cc_start: 0.7683 (m-30) cc_final: 0.7203 (m-30) REVERT: D 49 MET cc_start: 0.7419 (mtp) cc_final: 0.6568 (pp-130) REVERT: D 147 GLU cc_start: 0.7275 (tt0) cc_final: 0.7010 (tt0) REVERT: D 173 LYS cc_start: 0.7634 (mttm) cc_final: 0.7313 (mmtt) REVERT: D 227 MET cc_start: 0.6968 (mmt) cc_final: 0.6113 (mtp) REVERT: D 425 ARG cc_start: 0.6535 (ttt180) cc_final: 0.5909 (mtm-85) REVERT: E 470 MET cc_start: 0.5425 (mtp) cc_final: 0.4847 (mtt) REVERT: H 14 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6405 (tt0) REVERT: H 18 LYS cc_start: 0.6764 (tttt) cc_final: 0.6070 (tmmt) REVERT: H 30 ASP cc_start: 0.8226 (m-30) cc_final: 0.7986 (m-30) REVERT: H 49 MET cc_start: 0.7347 (mtp) cc_final: 0.6563 (tmm) REVERT: H 173 LYS cc_start: 0.7606 (mttm) cc_final: 0.7345 (mtpm) REVERT: H 227 MET cc_start: 0.7055 (mmt) cc_final: 0.5975 (ttp) REVERT: H 274 LYS cc_start: 0.7315 (mttt) cc_final: 0.7059 (mttp) REVERT: H 425 ARG cc_start: 0.6374 (ttt180) cc_final: 0.5973 (ttm110) REVERT: H 437 LEU cc_start: 0.7053 (mp) cc_final: 0.6811 (mp) REVERT: L 14 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6294 (tt0) REVERT: L 18 LYS cc_start: 0.6711 (tttt) cc_final: 0.6270 (mtpt) REVERT: L 49 MET cc_start: 0.7492 (mtp) cc_final: 0.6637 (pp-130) REVERT: L 147 GLU cc_start: 0.7291 (tt0) cc_final: 0.7015 (tt0) REVERT: L 227 MET cc_start: 0.6996 (mmt) cc_final: 0.5934 (ttp) REVERT: L 425 ARG cc_start: 0.6485 (ttt180) cc_final: 0.6075 (ttm110) REVERT: Q 14 GLU cc_start: 0.6469 (mt-10) cc_final: 0.6201 (tt0) REVERT: Q 18 LYS cc_start: 0.6726 (tttt) cc_final: 0.6092 (tmmt) REVERT: Q 48 ASP cc_start: 0.7574 (m-30) cc_final: 0.7122 (m-30) REVERT: Q 49 MET cc_start: 0.7391 (mtp) cc_final: 0.6682 (pp-130) REVERT: Q 147 GLU cc_start: 0.7288 (tt0) cc_final: 0.6955 (tt0) REVERT: Q 213 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7800 (ttp80) REVERT: Q 227 MET cc_start: 0.6967 (mmt) cc_final: 0.6061 (ttm) REVERT: Q 274 LYS cc_start: 0.7392 (mttt) cc_final: 0.7181 (mttp) REVERT: Q 425 ARG cc_start: 0.6491 (ttt180) cc_final: 0.5932 (mtm-85) outliers start: 5 outliers final: 0 residues processed: 266 average time/residue: 1.5335 time to fit residues: 456.0972 Evaluate side-chains 257 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN I 461 ASN R 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20730 Z= 0.205 Angle : 0.644 6.387 28250 Z= 0.348 Chirality : 0.048 0.197 3185 Planarity : 0.005 0.045 3485 Dihedral : 9.066 67.815 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.57 % Allowed : 7.52 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.03 (0.19), residues: 685 sheet: 1.19 (0.18), residues: 760 loop : 0.76 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 423 HIS 0.007 0.001 HIS D 107 PHE 0.022 0.002 PHE A 221 TYR 0.035 0.003 TYR L 299 ARG 0.010 0.001 ARG Q 28 *********************** 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 277 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 268 time to evaluate : 2.231 Fit side-chains REVERT: A 14 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6273 (tt0) REVERT: A 18 LYS cc_start: 0.6818 (tttt) cc_final: 0.6342 (mtmm) REVERT: A 49 MET cc_start: 0.7467 (mtp) cc_final: 0.6735 (pp-130) REVERT: A 68 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7801 (ttm110) REVERT: A 137 MET cc_start: 0.8079 (mmp) cc_final: 0.7605 (mmm) REVERT: A 213 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7837 (ttp80) REVERT: A 227 MET cc_start: 0.6830 (mmt) cc_final: 0.5739 (ttm) REVERT: A 425 ARG cc_start: 0.6456 (ttt180) cc_final: 0.6028 (ttm110) REVERT: D 14 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6445 (tt0) REVERT: D 18 LYS cc_start: 0.6825 (tttt) cc_final: 0.6355 (mtpt) REVERT: D 21 LYS cc_start: 0.6567 (tttm) cc_final: 0.6070 (tppt) REVERT: D 48 ASP cc_start: 0.7735 (m-30) cc_final: 0.7238 (m-30) REVERT: D 49 MET cc_start: 0.7425 (mtp) cc_final: 0.6491 (pp-130) REVERT: D 147 GLU cc_start: 0.7309 (tt0) cc_final: 0.7016 (tt0) REVERT: D 173 LYS cc_start: 0.7603 (mttm) cc_final: 0.7279 (mmtt) REVERT: D 227 MET cc_start: 0.7034 (mmt) cc_final: 0.6181 (mtp) REVERT: D 425 ARG cc_start: 0.6552 (ttt180) cc_final: 0.6054 (ttm110) REVERT: H 14 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6312 (tt0) REVERT: H 18 LYS cc_start: 0.6782 (tttt) cc_final: 0.6345 (mtpt) REVERT: H 30 ASP cc_start: 0.8330 (m-30) cc_final: 0.8037 (m-30) REVERT: H 49 MET cc_start: 0.7514 (mtp) cc_final: 0.6574 (tmm) REVERT: H 70 LYS cc_start: 0.8060 (mtmp) cc_final: 0.7837 (mttp) REVERT: H 173 LYS cc_start: 0.7597 (mttm) cc_final: 0.7309 (mtpm) REVERT: H 227 MET cc_start: 0.7067 (mmt) cc_final: 0.5979 (ttp) REVERT: H 425 ARG cc_start: 0.6409 (ttt180) cc_final: 0.6000 (ttm110) REVERT: H 437 LEU cc_start: 0.7070 (mp) cc_final: 0.6822 (mp) REVERT: L 14 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6346 (pt0) REVERT: L 49 MET cc_start: 0.7544 (mtp) cc_final: 0.6786 (tmm) REVERT: L 227 MET cc_start: 0.7088 (mmt) cc_final: 0.6044 (ttp) REVERT: L 268 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6144 (tt) REVERT: L 425 ARG cc_start: 0.6517 (ttt180) cc_final: 0.6088 (ttm110) REVERT: Q 14 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6281 (tt0) REVERT: Q 18 LYS cc_start: 0.6829 (tttt) cc_final: 0.6156 (tmmt) REVERT: Q 48 ASP cc_start: 0.7641 (m-30) cc_final: 0.7178 (m-30) REVERT: Q 49 MET cc_start: 0.7399 (mtp) cc_final: 0.6557 (pp-130) REVERT: Q 147 GLU cc_start: 0.7357 (tt0) cc_final: 0.7123 (tt0) REVERT: Q 213 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7836 (ttp80) REVERT: Q 227 MET cc_start: 0.6982 (mmt) cc_final: 0.6604 (mmp) REVERT: Q 425 ARG cc_start: 0.6526 (ttt180) cc_final: 0.6071 (ttm110) outliers start: 9 outliers final: 5 residues processed: 273 average time/residue: 1.5774 time to fit residues: 481.2930 Evaluate side-chains 266 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 260 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 439 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 M 417 ASN Q 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20730 Z= 0.172 Angle : 0.603 6.441 28250 Z= 0.325 Chirality : 0.047 0.209 3185 Planarity : 0.004 0.038 3485 Dihedral : 8.684 64.972 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.67 % Allowed : 7.48 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.16), residues: 2505 helix: 2.08 (0.19), residues: 685 sheet: 1.12 (0.18), residues: 775 loop : 0.87 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 423 HIS 0.004 0.001 HIS D 107 PHE 0.019 0.002 PHE A 221 TYR 0.031 0.002 TYR L 299 ARG 0.006 0.001 ARG H 141 *********************** 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 274 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 263 time to evaluate : 2.932 Fit side-chains REVERT: A 14 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6344 (tt0) REVERT: A 18 LYS cc_start: 0.6806 (tttt) cc_final: 0.6332 (mtmm) REVERT: A 49 MET cc_start: 0.7455 (mtp) cc_final: 0.6730 (pp-130) REVERT: A 68 ARG cc_start: 0.8247 (ttt-90) cc_final: 0.7809 (ttm110) REVERT: A 137 MET cc_start: 0.8050 (mmp) cc_final: 0.7586 (mmm) REVERT: A 227 MET cc_start: 0.6779 (mmt) cc_final: 0.5680 (ttp) REVERT: A 425 ARG cc_start: 0.6442 (ttt180) cc_final: 0.6025 (ttm110) REVERT: D 14 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6442 (tt0) REVERT: D 18 LYS cc_start: 0.6704 (tttt) cc_final: 0.6226 (mtpt) REVERT: D 21 LYS cc_start: 0.6576 (tttm) cc_final: 0.6077 (tppt) REVERT: D 48 ASP cc_start: 0.7723 (m-30) cc_final: 0.7227 (m-30) REVERT: D 49 MET cc_start: 0.7397 (mtp) cc_final: 0.6549 (pp-130) REVERT: D 147 GLU cc_start: 0.7309 (tt0) cc_final: 0.7007 (tt0) REVERT: D 173 LYS cc_start: 0.7595 (mttm) cc_final: 0.7290 (mmtt) REVERT: D 227 MET cc_start: 0.6994 (mmt) cc_final: 0.6146 (mtp) REVERT: D 425 ARG cc_start: 0.6542 (ttt180) cc_final: 0.5896 (mtm-85) REVERT: H 14 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6460 (tt0) REVERT: H 18 LYS cc_start: 0.6766 (tttt) cc_final: 0.6334 (mtpt) REVERT: H 30 ASP cc_start: 0.8354 (m-30) cc_final: 0.8061 (m-30) REVERT: H 49 MET cc_start: 0.7456 (mtp) cc_final: 0.6584 (pp-130) REVERT: H 70 LYS cc_start: 0.8062 (mtmp) cc_final: 0.7839 (mttp) REVERT: H 173 LYS cc_start: 0.7607 (mttm) cc_final: 0.7331 (mtpm) REVERT: H 227 MET cc_start: 0.7065 (mmt) cc_final: 0.5980 (ttp) REVERT: H 425 ARG cc_start: 0.6401 (ttt180) cc_final: 0.6006 (ttm110) REVERT: H 429 ILE cc_start: 0.6691 (tp) cc_final: 0.6337 (mm) REVERT: H 437 LEU cc_start: 0.7064 (mp) cc_final: 0.6825 (mp) REVERT: L 14 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6329 (pt0) REVERT: L 30 ASP cc_start: 0.8283 (m-30) cc_final: 0.8044 (m-30) REVERT: L 49 MET cc_start: 0.7586 (mtp) cc_final: 0.6713 (pp-130) REVERT: L 227 MET cc_start: 0.7082 (mmt) cc_final: 0.6035 (ttp) REVERT: L 268 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6173 (tt) REVERT: L 425 ARG cc_start: 0.6512 (ttt180) cc_final: 0.6082 (ttm110) REVERT: Q 14 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6302 (tt0) REVERT: Q 18 LYS cc_start: 0.6798 (tttt) cc_final: 0.6105 (tmmt) REVERT: Q 48 ASP cc_start: 0.7618 (m-30) cc_final: 0.7162 (m-30) REVERT: Q 49 MET cc_start: 0.7424 (mtp) cc_final: 0.6671 (pp-130) REVERT: Q 147 GLU cc_start: 0.7359 (tt0) cc_final: 0.7112 (tt0) REVERT: Q 213 ARG cc_start: 0.8115 (ttp-110) cc_final: 0.7822 (ttp80) REVERT: Q 227 MET cc_start: 0.6971 (mmt) cc_final: 0.6596 (mmp) REVERT: Q 425 ARG cc_start: 0.6510 (ttt180) cc_final: 0.5927 (mtm-85) outliers start: 11 outliers final: 6 residues processed: 269 average time/residue: 1.5456 time to fit residues: 465.1893 Evaluate side-chains 270 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 263 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 439 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20730 Z= 0.288 Angle : 0.744 7.244 28250 Z= 0.400 Chirality : 0.052 0.230 3185 Planarity : 0.006 0.061 3485 Dihedral : 9.486 68.654 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.76 % Allowed : 7.57 % Favored : 91.67 % 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: 1.66 (0.16), residues: 2505 helix: 1.72 (0.19), residues: 685 sheet: 1.04 (0.18), residues: 795 loop : 0.91 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 423 HIS 0.009 0.002 HIS D 107 PHE 0.028 0.003 PHE L 98 TYR 0.034 0.003 TYR L 299 ARG 0.013 0.001 ARG Q 28 *********************** 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 fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 2.292 Fit side-chains REVERT: A 14 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6367 (tt0) REVERT: A 49 MET cc_start: 0.7478 (mtp) cc_final: 0.6697 (pp-130) REVERT: A 227 MET cc_start: 0.6877 (mmt) cc_final: 0.5783 (ttm) REVERT: A 425 ARG cc_start: 0.6496 (ttt180) cc_final: 0.6073 (ttm110) REVERT: D 14 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6450 (tt0) REVERT: D 18 LYS cc_start: 0.6799 (tttt) cc_final: 0.6364 (mtmp) REVERT: D 21 LYS cc_start: 0.6615 (tttm) cc_final: 0.6121 (tppt) REVERT: D 48 ASP cc_start: 0.7741 (m-30) cc_final: 0.7240 (m-30) REVERT: D 49 MET cc_start: 0.7415 (mtp) cc_final: 0.6473 (pp-130) REVERT: D 173 LYS cc_start: 0.7590 (mttm) cc_final: 0.7274 (mmtt) REVERT: D 227 MET cc_start: 0.7004 (mmt) cc_final: 0.6012 (ttp) REVERT: D 425 ARG cc_start: 0.6524 (ttt180) cc_final: 0.6045 (ttm110) REVERT: H 14 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6382 (tt0) REVERT: H 18 LYS cc_start: 0.6801 (tttt) cc_final: 0.6377 (mtpt) REVERT: H 49 MET cc_start: 0.7504 (mtp) cc_final: 0.6557 (pp-130) REVERT: H 70 LYS cc_start: 0.8062 (mtmp) cc_final: 0.7836 (mttp) REVERT: H 173 LYS cc_start: 0.7579 (mttm) cc_final: 0.7292 (mtpm) REVERT: H 227 MET cc_start: 0.7093 (mmt) cc_final: 0.5997 (ttp) REVERT: H 268 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.6080 (tt) REVERT: H 425 ARG cc_start: 0.6446 (ttt180) cc_final: 0.6039 (ttm110) REVERT: H 429 ILE cc_start: 0.6685 (tp) cc_final: 0.6307 (mm) REVERT: L 14 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6364 (pt0) REVERT: L 30 ASP cc_start: 0.8280 (m-30) cc_final: 0.8043 (m-30) REVERT: L 49 MET cc_start: 0.7553 (mtp) cc_final: 0.6643 (pp-130) REVERT: L 227 MET cc_start: 0.7108 (mmt) cc_final: 0.6030 (ttp) REVERT: L 425 ARG cc_start: 0.6527 (ttt180) cc_final: 0.6086 (ttm110) REVERT: Q 14 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6373 (pt0) REVERT: Q 18 LYS cc_start: 0.6918 (tttt) cc_final: 0.6187 (tmmt) REVERT: Q 48 ASP cc_start: 0.7636 (m-30) cc_final: 0.7163 (m-30) REVERT: Q 49 MET cc_start: 0.7395 (mtp) cc_final: 0.6522 (pp-130) REVERT: Q 147 GLU cc_start: 0.7337 (tt0) cc_final: 0.7123 (tt0) REVERT: Q 213 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7839 (ttp80) REVERT: Q 227 MET cc_start: 0.7025 (mmt) cc_final: 0.6102 (mtp) REVERT: Q 425 ARG cc_start: 0.6536 (ttt180) cc_final: 0.6076 (ttm110) outliers start: 12 outliers final: 6 residues processed: 271 average time/residue: 1.5805 time to fit residues: 480.4196 Evaluate side-chains 269 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 262 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain M residue 439 SER 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 134 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 129 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 170 optimal weight: 0.0980 chunk 197 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 GLN Q 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20730 Z= 0.174 Angle : 0.616 7.507 28250 Z= 0.330 Chirality : 0.047 0.217 3185 Planarity : 0.004 0.038 3485 Dihedral : 8.835 65.241 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.71 % Allowed : 7.71 % Favored : 91.57 % 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: 1.98 (0.19), residues: 685 sheet: 1.16 (0.18), residues: 770 loop : 0.87 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 423 HIS 0.004 0.001 HIS H 191 PHE 0.019 0.002 PHE A 221 TYR 0.031 0.002 TYR D 299 ARG 0.006 0.001 ARG H 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5010 Ramachandran restraints generated. 2505 Oldfield, 0 Emsley, 2505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 265 time to evaluate : 1.895 Fit side-chains REVERT: A 14 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6308 (tt0) REVERT: A 18 LYS cc_start: 0.6803 (tttt) cc_final: 0.6340 (mtmm) REVERT: A 49 MET cc_start: 0.7485 (mtp) cc_final: 0.6749 (pp-130) REVERT: A 68 ARG cc_start: 0.8240 (ttt-90) cc_final: 0.7790 (ttm110) REVERT: A 137 MET cc_start: 0.8037 (mmp) cc_final: 0.7572 (mmm) REVERT: A 227 MET cc_start: 0.6857 (mmt) cc_final: 0.5739 (ttp) REVERT: A 425 ARG cc_start: 0.6433 (ttt180) cc_final: 0.6001 (ttm110) REVERT: D 14 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6367 (tt0) REVERT: D 18 LYS cc_start: 0.6663 (tttt) cc_final: 0.6144 (mtmm) REVERT: D 21 LYS cc_start: 0.6562 (tttm) cc_final: 0.6064 (tppt) REVERT: D 48 ASP cc_start: 0.7729 (m-30) cc_final: 0.7240 (m-30) REVERT: D 49 MET cc_start: 0.7401 (mtp) cc_final: 0.6560 (pp-130) REVERT: D 147 GLU cc_start: 0.7346 (tt0) cc_final: 0.7035 (tt0) REVERT: D 173 LYS cc_start: 0.7613 (mttm) cc_final: 0.7306 (mmtt) REVERT: D 227 MET cc_start: 0.7002 (mmt) cc_final: 0.5984 (ttp) REVERT: D 425 ARG cc_start: 0.6520 (ttt180) cc_final: 0.5892 (mtm-85) REVERT: H 14 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6460 (tt0) REVERT: H 18 LYS cc_start: 0.6823 (tttt) cc_final: 0.6405 (mtpt) REVERT: H 49 MET cc_start: 0.7492 (mtp) cc_final: 0.6633 (pp-130) REVERT: H 70 LYS cc_start: 0.8061 (mtmp) cc_final: 0.7849 (mttp) REVERT: H 173 LYS cc_start: 0.7606 (mttm) cc_final: 0.7329 (mtpm) REVERT: H 227 MET cc_start: 0.7068 (mmt) cc_final: 0.5973 (ttp) REVERT: H 268 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6142 (tt) REVERT: H 425 ARG cc_start: 0.6427 (ttt180) cc_final: 0.6024 (ttm110) REVERT: H 429 ILE cc_start: 0.6650 (tp) cc_final: 0.6295 (mm) REVERT: L 14 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6343 (pt0) REVERT: L 30 ASP cc_start: 0.8241 (m-30) cc_final: 0.8005 (m-30) REVERT: L 49 MET cc_start: 0.7584 (mtp) cc_final: 0.6714 (pp-130) REVERT: L 227 MET cc_start: 0.7088 (mmt) cc_final: 0.6034 (ttp) REVERT: L 425 ARG cc_start: 0.6488 (ttt180) cc_final: 0.6057 (ttm110) REVERT: Q 14 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6297 (tt0) REVERT: Q 18 LYS cc_start: 0.6836 (tttt) cc_final: 0.6139 (tmmt) REVERT: Q 48 ASP cc_start: 0.7602 (m-30) cc_final: 0.7149 (m-30) REVERT: Q 49 MET cc_start: 0.7429 (mtp) cc_final: 0.6659 (pp-130) REVERT: Q 147 GLU cc_start: 0.7308 (tt0) cc_final: 0.7065 (tt0) REVERT: Q 213 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7813 (ttp80) REVERT: Q 227 MET cc_start: 0.7001 (mmt) cc_final: 0.6112 (ttm) REVERT: Q 425 ARG cc_start: 0.6524 (ttt180) cc_final: 0.6065 (ttm110) outliers start: 10 outliers final: 6 residues processed: 269 average time/residue: 1.4749 time to fit residues: 445.1301 Evaluate side-chains 271 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 264 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 439 SER Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain M residue 439 SER 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 207 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 ASN M 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20730 Z= 0.193 Angle : 0.645 8.584 28250 Z= 0.344 Chirality : 0.048 0.222 3185 Planarity : 0.005 0.044 3485 Dihedral : 8.743 64.013 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.71 % Allowed : 7.71 % Favored : 91.57 % 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: 1.80 (0.16), residues: 2505 helix: 1.90 (0.19), residues: 685 sheet: 1.13 (0.18), residues: 795 loop : 0.93 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 423 HIS 0.005 0.001 HIS D 107 PHE 0.021 0.002 PHE A 221 TYR 0.032 0.002 TYR A 299 ARG 0.007 0.001 ARG H 213 *********************** 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 278 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 268 time to evaluate : 2.125 Fit side-chains REVERT: A 14 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6303 (tt0) REVERT: A 18 LYS cc_start: 0.6805 (tttt) cc_final: 0.6338 (mtmm) REVERT: A 49 MET cc_start: 0.7483 (mtp) cc_final: 0.6747 (pp-130) REVERT: A 68 ARG cc_start: 0.8232 (ttt-90) cc_final: 0.7777 (ttm110) REVERT: A 227 MET cc_start: 0.6859 (mmt) cc_final: 0.5779 (ttm) REVERT: A 425 ARG cc_start: 0.6458 (ttt180) cc_final: 0.6027 (ttm110) REVERT: D 14 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6447 (tt0) REVERT: D 18 LYS cc_start: 0.6768 (tttt) cc_final: 0.6369 (mtpt) REVERT: D 21 LYS cc_start: 0.6619 (tttm) cc_final: 0.6112 (tppt) REVERT: D 48 ASP cc_start: 0.7703 (m-30) cc_final: 0.7215 (m-30) REVERT: D 49 MET cc_start: 0.7402 (mtp) cc_final: 0.6582 (pp-130) REVERT: D 147 GLU cc_start: 0.7352 (tt0) cc_final: 0.7040 (tt0) REVERT: D 173 LYS cc_start: 0.7598 (mttm) cc_final: 0.7295 (mmtt) REVERT: D 227 MET cc_start: 0.7014 (mmt) cc_final: 0.5992 (ttp) REVERT: D 425 ARG cc_start: 0.6535 (ttt180) cc_final: 0.6055 (ttm110) REVERT: H 14 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6464 (tt0) REVERT: H 18 LYS cc_start: 0.6798 (tttt) cc_final: 0.6369 (mtpt) REVERT: H 49 MET cc_start: 0.7488 (mtp) cc_final: 0.6634 (pp-130) REVERT: H 70 LYS cc_start: 0.8070 (mtmp) cc_final: 0.7854 (mttp) REVERT: H 173 LYS cc_start: 0.7593 (mttm) cc_final: 0.7316 (mtpm) REVERT: H 213 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7678 (ttm110) REVERT: H 227 MET cc_start: 0.7057 (mmt) cc_final: 0.5969 (ttp) REVERT: H 268 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6169 (tt) REVERT: H 425 ARG cc_start: 0.6404 (ttt180) cc_final: 0.6012 (ttm110) REVERT: H 429 ILE cc_start: 0.6630 (tp) cc_final: 0.6271 (mm) REVERT: L 14 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6335 (pt0) REVERT: L 30 ASP cc_start: 0.8259 (m-30) cc_final: 0.8021 (m-30) REVERT: L 49 MET cc_start: 0.7598 (mtp) cc_final: 0.6723 (pp-130) REVERT: L 227 MET cc_start: 0.7113 (mmt) cc_final: 0.6054 (ttp) REVERT: L 425 ARG cc_start: 0.6507 (ttt180) cc_final: 0.6076 (ttm110) REVERT: Q 14 GLU cc_start: 0.6493 (mt-10) cc_final: 0.6275 (tt0) REVERT: Q 18 LYS cc_start: 0.6871 (tttt) cc_final: 0.6160 (tmmt) REVERT: Q 48 ASP cc_start: 0.7594 (m-30) cc_final: 0.7142 (m-30) REVERT: Q 49 MET cc_start: 0.7401 (mtp) cc_final: 0.6625 (pp-130) REVERT: Q 147 GLU cc_start: 0.7331 (tt0) cc_final: 0.7102 (tt0) REVERT: Q 213 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7843 (ttp80) REVERT: Q 227 MET cc_start: 0.6982 (mmt) cc_final: 0.6608 (mmp) REVERT: Q 425 ARG cc_start: 0.6541 (ttt180) cc_final: 0.6079 (ttm110) outliers start: 10 outliers final: 7 residues processed: 273 average time/residue: 1.4869 time to fit residues: 454.7804 Evaluate side-chains 274 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 266 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain E residue 470 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 206 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 137 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** Q 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20730 Z= 0.151 Angle : 0.586 8.162 28250 Z= 0.310 Chirality : 0.046 0.237 3185 Planarity : 0.004 0.034 3485 Dihedral : 8.174 59.686 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.57 % Allowed : 8.10 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.17), residues: 2505 helix: 2.08 (0.19), residues: 685 sheet: 1.26 (0.18), residues: 775 loop : 0.91 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 423 HIS 0.003 0.001 HIS H 191 PHE 0.017 0.002 PHE Q 221 TYR 0.033 0.002 TYR H 299 ARG 0.006 0.000 ARG H 213 ********************** 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 272 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 265 time to evaluate : 2.386 Fit side-chains REVERT: A 14 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6292 (tt0) REVERT: A 18 LYS cc_start: 0.6852 (tttt) cc_final: 0.6385 (mtmm) REVERT: A 49 MET cc_start: 0.7452 (mtp) cc_final: 0.6770 (pp-130) REVERT: A 68 ARG cc_start: 0.8246 (ttt-90) cc_final: 0.7782 (ttm110) REVERT: A 137 MET cc_start: 0.8059 (mmp) cc_final: 0.7585 (mmm) REVERT: A 227 MET cc_start: 0.6869 (mmt) cc_final: 0.5766 (ttp) REVERT: A 425 ARG cc_start: 0.6433 (ttt180) cc_final: 0.5998 (ttm110) REVERT: D 14 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6357 (tt0) REVERT: D 18 LYS cc_start: 0.6569 (tttt) cc_final: 0.6048 (mtmm) REVERT: D 21 LYS cc_start: 0.6513 (tttm) cc_final: 0.6048 (tppt) REVERT: D 48 ASP cc_start: 0.7656 (m-30) cc_final: 0.7178 (m-30) REVERT: D 49 MET cc_start: 0.7359 (mtp) cc_final: 0.6561 (pp-130) REVERT: D 147 GLU cc_start: 0.7359 (tt0) cc_final: 0.7037 (tt0) REVERT: D 173 LYS cc_start: 0.7621 (mttm) cc_final: 0.7320 (mmtt) REVERT: D 227 MET cc_start: 0.6981 (mmt) cc_final: 0.6135 (mtp) REVERT: D 425 ARG cc_start: 0.6499 (ttt180) cc_final: 0.5899 (mtm-85) REVERT: H 14 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6475 (tt0) REVERT: H 18 LYS cc_start: 0.6773 (tttt) cc_final: 0.6079 (tmmt) REVERT: H 49 MET cc_start: 0.7432 (mtp) cc_final: 0.6584 (pp-130) REVERT: H 173 LYS cc_start: 0.7638 (mttm) cc_final: 0.7365 (mtpm) REVERT: H 213 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7768 (ttm170) REVERT: H 227 MET cc_start: 0.7021 (mmt) cc_final: 0.5939 (ttp) REVERT: H 268 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6132 (tt) REVERT: H 425 ARG cc_start: 0.6414 (ttt180) cc_final: 0.6000 (ttm110) REVERT: L 14 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6341 (pt0) REVERT: L 30 ASP cc_start: 0.8232 (m-30) cc_final: 0.7985 (m-30) REVERT: L 49 MET cc_start: 0.7532 (mtp) cc_final: 0.6745 (pp-130) REVERT: L 227 MET cc_start: 0.7077 (mmt) cc_final: 0.6030 (ttp) REVERT: L 425 ARG cc_start: 0.6494 (ttt180) cc_final: 0.6071 (ttm110) REVERT: Q 14 GLU cc_start: 0.6499 (mt-10) cc_final: 0.6277 (tt0) REVERT: Q 18 LYS cc_start: 0.6789 (tttt) cc_final: 0.6087 (tmmt) REVERT: Q 48 ASP cc_start: 0.7495 (m-30) cc_final: 0.7050 (m-30) REVERT: Q 49 MET cc_start: 0.7405 (mtp) cc_final: 0.6669 (pp-130) REVERT: Q 147 GLU cc_start: 0.7317 (tt0) cc_final: 0.7076 (tt0) REVERT: Q 213 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7824 (ttp80) REVERT: Q 227 MET cc_start: 0.6974 (mmt) cc_final: 0.6605 (mmp) REVERT: Q 425 ARG cc_start: 0.6489 (ttt180) cc_final: 0.6036 (ttm110) outliers start: 7 outliers final: 4 residues processed: 269 average time/residue: 1.5048 time to fit residues: 453.9144 Evaluate side-chains 267 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 262 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 456 THR Chi-restraints excluded: chain L residue 268 LEU Chi-restraints excluded: chain M residue 483 CYS Chi-restraints excluded: chain R residue 483 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 156 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.195797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.148586 restraints weight = 107813.466| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 4.35 r_work: 0.3173 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work: 0.2992 rms_B_bonded: 3.88 restraints_weight: 0.1250 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20730 Z= 0.161 Angle : 0.600 8.599 28250 Z= 0.318 Chirality : 0.046 0.236 3185 Planarity : 0.004 0.037 3485 Dihedral : 8.029 57.504 3855 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.57 % Allowed : 8.14 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.16), residues: 2505 helix: 2.07 (0.19), residues: 685 sheet: 1.27 (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 I 423 HIS 0.003 0.001 HIS D 107 PHE 0.017 0.002 PHE H 221 TYR 0.031 0.002 TYR D 299 ARG 0.008 0.001 ARG L 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10373.77 seconds wall clock time: 185 minutes 3.36 seconds (11103.36 seconds total)