Starting phenix.real_space_refine on Sun Mar 17 23:07:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/03_2024/8pvb_17960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/03_2024/8pvb_17960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/03_2024/8pvb_17960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/03_2024/8pvb_17960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/03_2024/8pvb_17960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/03_2024/8pvb_17960_updated.pdb" } resolution = 3.6 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= 0.004 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 100 5.16 5 Cl 10 4.86 5 C 12530 2.51 5 N 3080 2.21 5 O 3505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 488": "NH1" <-> "NH2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H GLU 182": "OE1" <-> "OE2" Residue "H ARG 269": "NH1" <-> "NH2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "H PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 488": "NH1" <-> "NH2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 182": "OE1" <-> "OE2" Residue "L ARG 269": "NH1" <-> "NH2" Residue "L GLU 270": "OE1" <-> "OE2" Residue "L PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 312": "NH1" <-> "NH2" Residue "L TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "Q TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q GLU 182": "OE1" <-> "OE2" Residue "Q ARG 269": "NH1" <-> "NH2" Residue "Q GLU 270": "OE1" <-> "OE2" Residue "Q PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 312": "NH1" <-> "NH2" Residue "Q TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19225 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'R16': 1, 'V8D': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'R16': 1, 'V8D': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'R16': 1, 'V8D': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'R16': 1, 'V8D': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "Q" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 84 Unusual residues: {' CL': 2, 'D10': 4, 'HSM': 1, 'R16': 1, 'V8D': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb="CL CL A5407 " occ=0.20 residue: pdb="CL CL D5407 " occ=0.20 residue: pdb="CL CL H5407 " occ=0.20 residue: pdb="CL CL L5407 " occ=0.20 residue: pdb="CL CL Q5407 " occ=0.20 Time building chain proxies: 9.68, per 1000 atoms: 0.50 Number of scatterers: 19225 At special positions: 0 Unit cell: (142.416, 141.588, 125.856, 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 100 16.00 O 3505 8.00 N 3080 7.00 C 12530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.04 Simple disulfide: pdb=" SG CYS E 409 " - pdb=" SG CYS E 483 " distance=2.04 Simple disulfide: pdb=" SG CYS I 409 " - pdb=" SG CYS I 483 " distance=2.04 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.04 Simple disulfide: pdb=" SG CYS R 409 " - pdb=" SG CYS R 483 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 B 1 " - " ASN A 80 " " NAG C 1 " - " ASN A 149 " " NAG F 1 " - " ASN D 80 " " NAG G 1 " - " ASN D 149 " " NAG J 1 " - " ASN H 80 " " NAG K 1 " - " ASN H 149 " " NAG N 1 " - " ASN L 80 " " NAG P 1 " - " ASN L 149 " " NAG S 1 " - " ASN Q 80 " " NAG T 1 " - " ASN Q 149 " Time building additional restraints: 7.26 Conformation dependent library (CDL) restraints added in 3.3 seconds 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 35 sheets defined 29.9% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.690A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.808A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 310 through 446 removed outlier: 4.376A 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 451 No H-bonds generated for 'chain 'O' and resid 449 through 451' Processing helix chain 'O' and resid 496 through 498 No H-bonds generated for 'chain 'O' and resid 496 through 498' Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.690A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.809A pdb=" N THR D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 305 Processing helix chain 'D' and resid 310 through 446 removed outlier: 4.376A 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 451 No H-bonds generated for 'chain 'E' and resid 449 through 451' Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 85 through 90 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 219 through 224 Processing helix chain 'H' and resid 226 through 241 removed outlier: 3.690A pdb=" N TRP H 237 " --> pdb=" O THR H 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER H 239 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE H 240 " --> pdb=" O SER H 236 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP H 241 " --> pdb=" O TRP H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 271 removed outlier: 3.808A pdb=" N THR H 262 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR H 263 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR H 271 " --> pdb=" O HIS H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 305 Processing helix chain 'H' and resid 310 through 446 removed outlier: 4.376A 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 451 No H-bonds generated for 'chain 'I' and resid 449 through 451' Processing helix chain 'I' and resid 496 through 498 No H-bonds generated for 'chain 'I' and resid 496 through 498' Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'L' and resid 70 through 72 No H-bonds generated for 'chain 'L' and resid 70 through 72' Processing helix chain 'L' and resid 85 through 90 Processing helix chain 'L' and resid 171 through 173 No H-bonds generated for 'chain 'L' and resid 171 through 173' Processing helix chain 'L' and resid 178 through 180 No H-bonds generated for 'chain 'L' and resid 178 through 180' Processing helix chain 'L' and resid 219 through 224 Processing helix chain 'L' and resid 226 through 241 removed outlier: 3.690A pdb=" N TRP L 237 " --> pdb=" O THR L 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL L 238 " --> pdb=" O ILE L 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER L 239 " --> pdb=" O LEU L 235 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE L 240 " --> pdb=" O SER L 236 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP L 241 " --> pdb=" O TRP L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 271 removed outlier: 3.809A pdb=" N THR L 262 " --> pdb=" O VAL L 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR L 263 " --> pdb=" O LEU L 259 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR L 271 " --> pdb=" O HIS L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 305 Processing helix chain 'L' and resid 310 through 446 removed outlier: 4.376A 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 451 No H-bonds generated for 'chain 'M' and resid 449 through 451' Processing helix chain 'M' and resid 496 through 498 No H-bonds generated for 'chain 'M' and resid 496 through 498' Processing helix chain 'Q' and resid 9 through 20 Processing helix chain 'Q' and resid 70 through 72 No H-bonds generated for 'chain 'Q' and resid 70 through 72' Processing helix chain 'Q' and resid 85 through 90 Processing helix chain 'Q' and resid 171 through 173 No H-bonds generated for 'chain 'Q' and resid 171 through 173' Processing helix chain 'Q' and resid 178 through 180 No H-bonds generated for 'chain 'Q' and resid 178 through 180' Processing helix chain 'Q' and resid 219 through 224 Processing helix chain 'Q' and resid 226 through 241 removed outlier: 3.690A pdb=" N TRP Q 237 " --> pdb=" O THR Q 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL Q 238 " --> pdb=" O ILE Q 234 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER Q 239 " --> pdb=" O LEU Q 235 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE Q 240 " --> pdb=" O SER Q 236 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TRP Q 241 " --> pdb=" O TRP Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 271 removed outlier: 3.808A pdb=" N THR Q 262 " --> pdb=" O VAL Q 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR Q 263 " --> pdb=" O LEU Q 259 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR Q 271 " --> pdb=" O HIS Q 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 305 Processing helix chain 'Q' and resid 310 through 446 removed outlier: 4.376A 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 451 No H-bonds generated for 'chain 'R' and resid 449 through 451' Processing helix chain 'R' and resid 496 through 498 No H-bonds generated for 'chain 'R' and resid 496 through 498' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.325A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.906A pdb=" N MET A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.811A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'O' and resid 2 through 7 Processing sheet with id= F, first strand: chain 'O' and resid 506 through 508 removed outlier: 3.765A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'O' and resid 484 through 486 removed outlier: 3.812A pdb=" N TYR O 501 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.325A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.906A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.809A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 2 through 7 Processing sheet with id= M, first strand: chain 'E' and resid 506 through 508 removed outlier: 3.764A pdb=" N ILE E 420 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG E 425 " --> pdb=" O PHE E 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE E 434 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 484 through 486 removed outlier: 3.812A pdb=" N TYR E 501 " --> pdb=" O ALA E 485 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 164 through 168 removed outlier: 6.325A pdb=" N VAL H 36 " --> pdb=" O GLU H 165 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR H 167 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL H 38 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N CYS H 37 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG H 68 " --> pdb=" O CYS H 37 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR H 60 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE H 47 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR H 58 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE H 116 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.906A pdb=" N MET H 49 " --> pdb=" O THR H 58 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER H 156 " --> pdb=" O PRO H 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU H 190 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS H 215 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE H 188 " --> pdb=" O LYS H 215 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.810A pdb=" N THR H 133 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER H 104 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR H 131 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 2 through 7 Processing sheet with id= T, first strand: chain 'I' and resid 506 through 508 removed outlier: 3.765A pdb=" N ILE I 420 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG I 425 " --> pdb=" O PHE I 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE I 434 " --> pdb=" O ARG I 425 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 484 through 486 removed outlier: 3.812A pdb=" N TYR I 501 " --> pdb=" O ALA I 485 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 164 through 168 removed outlier: 6.325A pdb=" N VAL L 36 " --> pdb=" O GLU L 165 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR L 167 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL L 38 " --> pdb=" O TYR L 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N CYS L 37 " --> pdb=" O ARG L 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG L 68 " --> pdb=" O CYS L 37 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR L 60 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE L 47 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR L 58 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE L 116 " --> pdb=" O LEU L 83 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 49 through 51 removed outlier: 3.906A pdb=" N MET L 49 " --> pdb=" O THR L 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.631A pdb=" N SER L 156 " --> pdb=" O PRO L 206 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU L 190 " --> pdb=" O ARG L 213 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS L 215 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE L 188 " --> pdb=" O LYS L 215 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.810A pdb=" N THR L 133 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER L 104 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR L 131 " --> pdb=" O SER L 104 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 2 through 7 Processing sheet with id= AA, first strand: chain 'M' and resid 506 through 508 removed outlier: 3.765A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 484 through 486 removed outlier: 3.812A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 164 through 168 removed outlier: 6.325A pdb=" N VAL Q 36 " --> pdb=" O GLU Q 165 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR Q 167 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL Q 38 " --> pdb=" O TYR Q 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N CYS Q 37 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG Q 68 " --> pdb=" O CYS Q 37 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR Q 60 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE Q 47 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR Q 58 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE Q 116 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 49 through 51 removed outlier: 3.906A pdb=" N MET Q 49 " --> pdb=" O THR Q 58 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.630A pdb=" N SER Q 156 " --> pdb=" O PRO Q 206 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU Q 190 " --> pdb=" O ARG Q 213 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS Q 215 " --> pdb=" O ILE Q 188 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE Q 188 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.811A pdb=" N THR Q 133 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER Q 104 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR Q 131 " --> pdb=" O SER Q 104 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 2 through 7 Processing sheet with id= AH, first strand: chain 'R' and resid 506 through 508 removed outlier: 3.765A pdb=" N ILE R 420 " --> pdb=" O LYS R 486 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG R 425 " --> pdb=" O PHE R 434 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE R 434 " --> pdb=" O ARG R 425 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'R' and resid 484 through 486 removed outlier: 3.812A pdb=" N TYR R 501 " --> pdb=" O ALA R 485 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2385 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: 6.02 Time building geometry restraints manager: 7.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3418 1.33 - 1.46: 5988 1.46 - 1.58: 10104 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 19680 Sorted by residual: bond pdb=" CG HIS A 119 " pdb=" CD2 HIS A 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" CG HIS Q 119 " pdb=" CD2 HIS Q 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.91e+01 bond pdb=" CG HIS H 119 " pdb=" CD2 HIS H 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.90e+01 bond pdb=" CG HIS L 119 " pdb=" CD2 HIS L 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.90e+01 bond pdb=" CG HIS D 119 " pdb=" CD2 HIS D 119 " ideal model delta sigma weight residual 1.354 1.306 0.048 1.10e-02 8.26e+03 1.88e+01 ... (remaining 19675 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.32: 385 105.32 - 112.67: 8207 112.67 - 120.02: 10291 120.02 - 127.38: 7521 127.38 - 134.73: 226 Bond angle restraints: 26630 Sorted by residual: angle pdb=" CA ASP A 101 " pdb=" CB ASP A 101 " pdb=" CG ASP A 101 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.00e+00 1.00e+00 4.45e+01 angle pdb=" CA ASP Q 101 " pdb=" CB ASP Q 101 " pdb=" CG ASP Q 101 " ideal model delta sigma weight residual 112.60 119.25 -6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" CA ASP D 101 " pdb=" CB ASP D 101 " pdb=" CG ASP D 101 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA ASP L 101 " pdb=" CB ASP L 101 " pdb=" CG ASP L 101 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA ASP H 101 " pdb=" CB ASP H 101 " pdb=" CG ASP H 101 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.39e+01 ... (remaining 26625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.75: 11074 20.75 - 41.49: 646 41.49 - 62.24: 135 62.24 - 82.98: 70 82.98 - 103.73: 25 Dihedral angle restraints: 11950 sinusoidal: 5300 harmonic: 6650 Sorted by residual: 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 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER H 46 " pdb=" C SER H 46 " pdb=" N ILE H 47 " pdb=" CA ILE H 47 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 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 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 11947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1407 0.055 - 0.110: 955 0.110 - 0.165: 480 0.165 - 0.219: 135 0.219 - 0.274: 18 Chirality restraints: 2995 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 2.28 0.12 2.00e-02 2.50e+03 3.74e+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 2.28 0.12 2.00e-02 2.50e+03 3.68e+01 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.62e+01 ... (remaining 2992 not shown) Planarity restraints: 3270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.057 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" C7 NAG F 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.075 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.057 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" C7 NAG N 2 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.075 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.056 2.00e-02 2.50e+03 4.67e-02 2.73e+01 pdb=" C7 NAG J 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.075 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.009 2.00e-02 2.50e+03 ... (remaining 3267 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 0 1.96 - 2.94: 7536 2.94 - 3.92: 50717 3.92 - 4.90: 101895 Warning: very small nonbonded interaction distances. Nonbonded interactions: 160158 Sorted by model distance: nonbonded pdb="CL CL A5407 " pdb="CL CL D5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL H5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL L5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL A5407 " pdb="CL CL Q5407 " model vdw 0.000 3.340 nonbonded pdb="CL CL D5407 " pdb="CL CL H5407 " model vdw 0.000 3.340 ... (remaining 160153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'Q' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.780 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: 7.490 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 49.320 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.010 0.065 19680 Z= 0.675 Angle : 1.701 9.123 26630 Z= 1.129 Chirality : 0.086 0.274 2995 Planarity : 0.012 0.135 3260 Dihedral : 16.051 103.727 7705 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.27 % Allowed : 5.22 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -0.14 (0.17), residues: 2245 helix: -0.65 (0.18), residues: 615 sheet: 0.50 (0.20), residues: 645 loop : 0.07 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP L 237 HIS 0.009 0.002 HIS A 119 PHE 0.040 0.008 PHE H 221 TYR 0.043 0.007 TYR L 299 ARG 0.056 0.005 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 406 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 VAL cc_start: 0.8142 (t) cc_final: 0.7937 (m) REVERT: A 51 SER cc_start: 0.7489 (t) cc_final: 0.6681 (p) REVERT: A 99 LEU cc_start: 0.8533 (tt) cc_final: 0.8292 (tt) REVERT: A 139 ASP cc_start: 0.7484 (t0) cc_final: 0.7039 (p0) REVERT: A 148 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7377 (mm110) REVERT: A 163 ASP cc_start: 0.7616 (m-30) cc_final: 0.7041 (m-30) REVERT: A 190 GLU cc_start: 0.7612 (tt0) cc_final: 0.7297 (tt0) REVERT: A 213 ARG cc_start: 0.6899 (ttp-110) cc_final: 0.6652 (tpp80) REVERT: A 283 MET cc_start: 0.8210 (mmm) cc_final: 0.7866 (mmt) REVERT: D 12 VAL cc_start: 0.8217 (t) cc_final: 0.7890 (m) REVERT: D 41 ASN cc_start: 0.8235 (m110) cc_final: 0.7951 (m-40) REVERT: D 51 SER cc_start: 0.7687 (t) cc_final: 0.6826 (p) REVERT: D 139 ASP cc_start: 0.7445 (t0) cc_final: 0.7034 (p0) REVERT: D 148 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7284 (mm-40) REVERT: D 155 GLU cc_start: 0.8540 (tt0) cc_final: 0.8275 (tt0) REVERT: D 163 ASP cc_start: 0.7610 (m-30) cc_final: 0.7123 (m-30) REVERT: D 190 GLU cc_start: 0.7467 (tt0) cc_final: 0.7162 (tt0) REVERT: D 213 ARG cc_start: 0.6889 (ttp-110) cc_final: 0.6620 (tpp80) REVERT: D 301 PHE cc_start: 0.7842 (t80) cc_final: 0.7631 (t80) REVERT: D 425 ARG cc_start: 0.7384 (ttt180) cc_final: 0.7072 (ttp-110) REVERT: H 16 VAL cc_start: 0.8085 (t) cc_final: 0.7859 (m) REVERT: H 51 SER cc_start: 0.7679 (t) cc_final: 0.6669 (p) REVERT: H 139 ASP cc_start: 0.7462 (t0) cc_final: 0.6918 (p0) REVERT: H 147 GLU cc_start: 0.6541 (tt0) cc_final: 0.6235 (mm-30) REVERT: H 148 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7347 (mm-40) REVERT: H 155 GLU cc_start: 0.8581 (tt0) cc_final: 0.8250 (tt0) REVERT: H 163 ASP cc_start: 0.7605 (m-30) cc_final: 0.7296 (m-30) REVERT: H 190 GLU cc_start: 0.7607 (tt0) cc_final: 0.7280 (tt0) REVERT: H 213 ARG cc_start: 0.6906 (ttp-110) cc_final: 0.6408 (tpp80) REVERT: H 283 MET cc_start: 0.8229 (mmm) cc_final: 0.7989 (mmt) REVERT: H 301 PHE cc_start: 0.7944 (t80) cc_final: 0.7730 (t80) REVERT: L 16 VAL cc_start: 0.8174 (t) cc_final: 0.7932 (m) REVERT: L 41 ASN cc_start: 0.8240 (m110) cc_final: 0.7785 (m110) REVERT: L 51 SER cc_start: 0.7616 (t) cc_final: 0.6633 (p) REVERT: L 61 MET cc_start: 0.9039 (ptt) cc_final: 0.8805 (ptt) REVERT: L 139 ASP cc_start: 0.7590 (t0) cc_final: 0.7130 (p0) REVERT: L 144 PRO cc_start: 0.8620 (OUTLIER) cc_final: 0.8398 (Cg_endo) REVERT: L 148 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7393 (mm-40) REVERT: L 153 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8037 (mm-30) REVERT: L 155 GLU cc_start: 0.8538 (tt0) cc_final: 0.8090 (tt0) REVERT: L 163 ASP cc_start: 0.7732 (m-30) cc_final: 0.7408 (m-30) REVERT: L 190 GLU cc_start: 0.7622 (tt0) cc_final: 0.7259 (tt0) REVERT: L 213 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6694 (tpp80) REVERT: L 303 ASN cc_start: 0.8135 (t0) cc_final: 0.7899 (t0) REVERT: L 425 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7174 (ttp-170) REVERT: Q 41 ASN cc_start: 0.8261 (m110) cc_final: 0.7911 (m-40) REVERT: Q 43 ASP cc_start: 0.8305 (t70) cc_final: 0.8069 (t70) REVERT: Q 51 SER cc_start: 0.7523 (t) cc_final: 0.6585 (p) REVERT: Q 139 ASP cc_start: 0.7474 (t0) cc_final: 0.7097 (p0) REVERT: Q 153 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8120 (mm-30) REVERT: Q 163 ASP cc_start: 0.7598 (m-30) cc_final: 0.7157 (m-30) REVERT: Q 180 ARG cc_start: 0.7037 (mtt90) cc_final: 0.6674 (mtt180) REVERT: Q 190 GLU cc_start: 0.7631 (tt0) cc_final: 0.7322 (tt0) REVERT: Q 224 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8124 (mm-40) REVERT: Q 227 MET cc_start: 0.7599 (ttm) cc_final: 0.7325 (ttp) REVERT: Q 425 ARG cc_start: 0.7405 (ttt180) cc_final: 0.7081 (ttp-170) outliers start: 25 outliers final: 16 residues processed: 426 average time/residue: 0.3502 time to fit residues: 216.7884 Evaluate side-chains 319 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 301 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain D residue 144 PRO Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 144 PRO Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain M residue 459 ARG Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 0.0670 chunk 176 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 185 GLN D 185 GLN H 41 ASN H 185 GLN L 185 GLN L 265 ASN Q 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19680 Z= 0.176 Angle : 0.595 6.887 26630 Z= 0.315 Chirality : 0.047 0.171 2995 Planarity : 0.004 0.036 3260 Dihedral : 11.165 75.636 3589 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.82 % Allowed : 6.94 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.05 (0.18), residues: 2245 helix: 1.46 (0.20), residues: 610 sheet: 0.51 (0.19), residues: 685 loop : 0.52 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 440 HIS 0.003 0.001 HIS D 267 PHE 0.015 0.002 PHE L 306 TYR 0.029 0.002 TYR L 299 ARG 0.004 0.001 ARG Q 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.7512 (t) cc_final: 0.6591 (p) REVERT: A 55 MET cc_start: 0.7456 (mtp) cc_final: 0.6977 (mtt) REVERT: A 64 GLN cc_start: 0.7436 (mp10) cc_final: 0.6998 (mt0) REVERT: A 139 ASP cc_start: 0.7327 (t0) cc_final: 0.6805 (p0) REVERT: A 147 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6399 (mm-30) REVERT: A 148 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7441 (mm-40) REVERT: A 163 ASP cc_start: 0.7662 (m-30) cc_final: 0.7200 (m-30) REVERT: A 190 GLU cc_start: 0.7621 (tt0) cc_final: 0.7213 (tt0) REVERT: A 223 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7537 (tm) REVERT: A 235 LEU cc_start: 0.8504 (tp) cc_final: 0.8303 (tt) REVERT: A 425 ARG cc_start: 0.7761 (ttp-170) cc_final: 0.7367 (mtm-85) REVERT: D 51 SER cc_start: 0.7634 (t) cc_final: 0.6843 (p) REVERT: D 64 GLN cc_start: 0.7487 (mp10) cc_final: 0.7053 (mt0) REVERT: D 139 ASP cc_start: 0.7481 (t0) cc_final: 0.7066 (p0) REVERT: D 148 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7438 (mm-40) REVERT: D 163 ASP cc_start: 0.7425 (m-30) cc_final: 0.7023 (m-30) REVERT: D 190 GLU cc_start: 0.7517 (tt0) cc_final: 0.7166 (tt0) REVERT: D 213 ARG cc_start: 0.6958 (ttp-110) cc_final: 0.6666 (tpp80) REVERT: D 223 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7754 (tm) REVERT: H 51 SER cc_start: 0.7577 (t) cc_final: 0.6721 (p) REVERT: H 64 GLN cc_start: 0.7435 (mp10) cc_final: 0.7030 (mt0) REVERT: H 139 ASP cc_start: 0.7465 (t0) cc_final: 0.6897 (p0) REVERT: H 148 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7586 (mm-40) REVERT: H 155 GLU cc_start: 0.8383 (tt0) cc_final: 0.7917 (tt0) REVERT: H 179 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6873 (pp20) REVERT: H 190 GLU cc_start: 0.7638 (tt0) cc_final: 0.7284 (tt0) REVERT: H 213 ARG cc_start: 0.6822 (ttp-110) cc_final: 0.6573 (tpp80) REVERT: H 223 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7646 (tm) REVERT: H 425 ARG cc_start: 0.7584 (ttp-170) cc_final: 0.7172 (mtp-110) REVERT: L 41 ASN cc_start: 0.8115 (m110) cc_final: 0.7766 (m110) REVERT: L 51 SER cc_start: 0.7498 (t) cc_final: 0.6558 (p) REVERT: L 64 GLN cc_start: 0.7548 (mp10) cc_final: 0.7039 (mt0) REVERT: L 139 ASP cc_start: 0.7456 (t0) cc_final: 0.7045 (p0) REVERT: L 190 GLU cc_start: 0.7710 (tt0) cc_final: 0.7337 (tt0) REVERT: L 213 ARG cc_start: 0.6930 (ttp-110) cc_final: 0.6725 (tpp80) REVERT: L 223 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7627 (tm) REVERT: L 303 ASN cc_start: 0.8164 (t0) cc_final: 0.7883 (t0) REVERT: Q 51 SER cc_start: 0.7368 (t) cc_final: 0.6486 (p) REVERT: Q 64 GLN cc_start: 0.7375 (mp10) cc_final: 0.6897 (mt0) REVERT: Q 139 ASP cc_start: 0.7438 (t0) cc_final: 0.7101 (p0) REVERT: Q 163 ASP cc_start: 0.7558 (m-30) cc_final: 0.7265 (m-30) REVERT: Q 190 GLU cc_start: 0.7541 (tt0) cc_final: 0.7232 (tt0) REVERT: Q 223 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7642 (tm) REVERT: Q 224 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6616 (mp10) outliers start: 36 outliers final: 25 residues processed: 333 average time/residue: 0.3516 time to fit residues: 172.2230 Evaluate side-chains 303 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain O residue 459 ARG Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain M residue 459 ARG Chi-restraints excluded: chain Q residue 162 ASP Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 182 optimal weight: 0.0870 chunk 202 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 41 ASN D 185 GLN H 41 ASN Q 41 ASN Q 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 19680 Z= 0.227 Angle : 0.557 6.581 26630 Z= 0.296 Chirality : 0.046 0.181 2995 Planarity : 0.004 0.037 3260 Dihedral : 10.375 70.877 3583 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.23 % Allowed : 8.91 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.25 (0.18), residues: 2245 helix: 1.68 (0.20), residues: 615 sheet: 0.64 (0.19), residues: 685 loop : 0.57 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 443 HIS 0.002 0.001 HIS M 414 PHE 0.017 0.002 PHE O 424 TYR 0.029 0.002 TYR D 299 ARG 0.004 0.000 ARG Q 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 281 time to evaluate : 2.056 Fit side-chains REVERT: A 51 SER cc_start: 0.7554 (t) cc_final: 0.6779 (p) REVERT: A 64 GLN cc_start: 0.7334 (mp10) cc_final: 0.6982 (mt0) REVERT: A 139 ASP cc_start: 0.7472 (t0) cc_final: 0.6867 (p0) REVERT: A 163 ASP cc_start: 0.7761 (m-30) cc_final: 0.7348 (m-30) REVERT: A 190 GLU cc_start: 0.7544 (tt0) cc_final: 0.7226 (tt0) REVERT: A 223 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7675 (tm) REVERT: A 425 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.7313 (mtm-85) REVERT: O 421 MET cc_start: 0.7258 (mmm) cc_final: 0.6125 (mmm) REVERT: O 470 MET cc_start: 0.3558 (mpp) cc_final: 0.3310 (mtm) REVERT: D 51 SER cc_start: 0.7545 (t) cc_final: 0.6838 (p) REVERT: D 64 GLN cc_start: 0.7399 (mp10) cc_final: 0.7032 (mt0) REVERT: D 66 TYR cc_start: 0.7890 (m-80) cc_final: 0.7665 (m-80) REVERT: D 139 ASP cc_start: 0.7511 (t0) cc_final: 0.7105 (p0) REVERT: D 148 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7446 (mm110) REVERT: D 163 ASP cc_start: 0.7697 (m-30) cc_final: 0.7484 (m-30) REVERT: D 190 GLU cc_start: 0.7569 (tt0) cc_final: 0.7224 (tt0) REVERT: D 213 ARG cc_start: 0.6929 (ttp-110) cc_final: 0.6682 (tpp80) REVERT: D 223 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7859 (tm) REVERT: D 298 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7687 (tm-30) REVERT: H 40 MET cc_start: 0.8929 (mtt) cc_final: 0.8365 (mtt) REVERT: H 51 SER cc_start: 0.7541 (t) cc_final: 0.6617 (p) REVERT: H 64 GLN cc_start: 0.7280 (mp10) cc_final: 0.6997 (mt0) REVERT: H 139 ASP cc_start: 0.7571 (t0) cc_final: 0.6915 (p0) REVERT: H 179 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6762 (pp20) REVERT: H 190 GLU cc_start: 0.7678 (tt0) cc_final: 0.7309 (tt0) REVERT: H 223 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7743 (tm) REVERT: H 425 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.7181 (mtm-85) REVERT: L 51 SER cc_start: 0.7575 (t) cc_final: 0.6780 (p) REVERT: L 64 GLN cc_start: 0.7512 (mp10) cc_final: 0.7080 (mt0) REVERT: L 139 ASP cc_start: 0.7537 (t0) cc_final: 0.6973 (p0) REVERT: L 155 GLU cc_start: 0.8511 (tt0) cc_final: 0.8095 (tt0) REVERT: L 190 GLU cc_start: 0.7762 (tt0) cc_final: 0.7428 (tt0) REVERT: L 223 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7832 (tm) REVERT: L 298 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7966 (tm-30) REVERT: Q 51 SER cc_start: 0.7632 (t) cc_final: 0.6866 (p) REVERT: Q 64 GLN cc_start: 0.7260 (mp10) cc_final: 0.6908 (mt0) REVERT: Q 139 ASP cc_start: 0.7487 (t0) cc_final: 0.7106 (p0) REVERT: Q 190 GLU cc_start: 0.7531 (tt0) cc_final: 0.7273 (tt0) REVERT: Q 223 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7860 (tm) REVERT: Q 224 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: R 421 MET cc_start: 0.7245 (mmm) cc_final: 0.6207 (mmm) outliers start: 44 outliers final: 28 residues processed: 313 average time/residue: 0.3289 time to fit residues: 152.8961 Evaluate side-chains 288 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 254 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 97 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 217 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN H 41 ASN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19680 Z= 0.164 Angle : 0.510 6.407 26630 Z= 0.269 Chirality : 0.044 0.209 2995 Planarity : 0.003 0.036 3260 Dihedral : 9.446 63.761 3563 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.87 % Allowed : 9.22 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.34 (0.18), residues: 2245 helix: 1.88 (0.20), residues: 615 sheet: 0.72 (0.19), residues: 685 loop : 0.50 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 67 HIS 0.003 0.001 HIS H 267 PHE 0.015 0.001 PHE R 424 TYR 0.029 0.001 TYR D 299 ARG 0.005 0.000 ARG Q 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 277 time to evaluate : 2.059 Fit side-chains REVERT: A 51 SER cc_start: 0.7610 (t) cc_final: 0.6892 (p) REVERT: A 55 MET cc_start: 0.7477 (mtp) cc_final: 0.7143 (mtt) REVERT: A 64 GLN cc_start: 0.7322 (mp10) cc_final: 0.7003 (mt0) REVERT: A 139 ASP cc_start: 0.7516 (t0) cc_final: 0.6857 (p0) REVERT: A 148 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7456 (mm110) REVERT: A 163 ASP cc_start: 0.7762 (m-30) cc_final: 0.7341 (m-30) REVERT: A 190 GLU cc_start: 0.7552 (tt0) cc_final: 0.7268 (tt0) REVERT: A 223 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7818 (tm) REVERT: A 425 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7306 (mtm-85) REVERT: D 51 SER cc_start: 0.7638 (t) cc_final: 0.6871 (p) REVERT: D 64 GLN cc_start: 0.7316 (mp10) cc_final: 0.7048 (mt0) REVERT: D 139 ASP cc_start: 0.7540 (t0) cc_final: 0.7012 (p0) REVERT: D 148 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7453 (mm-40) REVERT: D 163 ASP cc_start: 0.7707 (m-30) cc_final: 0.7489 (m-30) REVERT: D 190 GLU cc_start: 0.7602 (tt0) cc_final: 0.7238 (tt0) REVERT: D 213 ARG cc_start: 0.6833 (ttp-110) cc_final: 0.6598 (tpp80) REVERT: D 223 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7860 (tm) REVERT: D 298 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7928 (tm-30) REVERT: H 51 SER cc_start: 0.7597 (t) cc_final: 0.6752 (p) REVERT: H 64 GLN cc_start: 0.7278 (mp10) cc_final: 0.6987 (mt0) REVERT: H 139 ASP cc_start: 0.7596 (t0) cc_final: 0.6936 (p0) REVERT: H 179 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6665 (pp20) REVERT: H 190 GLU cc_start: 0.7621 (tt0) cc_final: 0.7347 (tt0) REVERT: H 425 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.7245 (mtm-85) REVERT: L 51 SER cc_start: 0.7728 (t) cc_final: 0.6931 (p) REVERT: L 64 GLN cc_start: 0.7466 (mp10) cc_final: 0.7113 (mt0) REVERT: L 139 ASP cc_start: 0.7443 (t0) cc_final: 0.6933 (p0) REVERT: L 190 GLU cc_start: 0.7687 (tt0) cc_final: 0.7403 (tt0) REVERT: L 223 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7866 (tm) REVERT: L 298 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8030 (tm-30) REVERT: M 421 MET cc_start: 0.7369 (mmm) cc_final: 0.6139 (mmm) REVERT: Q 51 SER cc_start: 0.7578 (t) cc_final: 0.6753 (p) REVERT: Q 64 GLN cc_start: 0.7240 (mp10) cc_final: 0.6969 (mt0) REVERT: Q 68 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7511 (ttm170) REVERT: Q 139 ASP cc_start: 0.7418 (t0) cc_final: 0.6994 (p0) REVERT: Q 190 GLU cc_start: 0.7599 (tt0) cc_final: 0.7319 (tt0) REVERT: Q 223 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7641 (tm) REVERT: Q 224 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.6278 (mp10) outliers start: 37 outliers final: 29 residues processed: 300 average time/residue: 0.3368 time to fit residues: 151.0916 Evaluate side-chains 285 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 251 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 0.0980 chunk 123 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN D 303 ASN H 303 ASN L 185 GLN Q 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19680 Z= 0.327 Angle : 0.606 6.646 26630 Z= 0.318 Chirality : 0.048 0.200 2995 Planarity : 0.005 0.036 3260 Dihedral : 9.993 62.002 3561 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.29 % Allowed : 9.47 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.76 (0.17), residues: 2245 helix: 1.36 (0.20), residues: 615 sheet: 0.40 (0.19), residues: 665 loop : 0.16 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 241 HIS 0.004 0.001 HIS Q 267 PHE 0.018 0.002 PHE A 98 TYR 0.027 0.002 TYR H 299 ARG 0.004 0.001 ARG L 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 268 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.7579 (t) cc_final: 0.6870 (p) REVERT: A 64 GLN cc_start: 0.7489 (mp10) cc_final: 0.7082 (mt0) REVERT: A 139 ASP cc_start: 0.7473 (t0) cc_final: 0.6847 (p0) REVERT: A 142 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7527 (mtm180) REVERT: A 190 GLU cc_start: 0.7529 (tt0) cc_final: 0.7224 (tt0) REVERT: A 223 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7871 (tm) REVERT: A 425 ARG cc_start: 0.7604 (ttp-170) cc_final: 0.7264 (mtm-85) REVERT: O 421 MET cc_start: 0.7352 (mmm) cc_final: 0.6437 (mmm) REVERT: D 51 SER cc_start: 0.7602 (t) cc_final: 0.6886 (p) REVERT: D 64 GLN cc_start: 0.7464 (mp10) cc_final: 0.7043 (mt0) REVERT: D 139 ASP cc_start: 0.7572 (t0) cc_final: 0.6864 (p0) REVERT: D 190 GLU cc_start: 0.7547 (tt0) cc_final: 0.7148 (tt0) REVERT: D 223 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7769 (tm) REVERT: D 298 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7858 (tm-30) REVERT: H 51 SER cc_start: 0.7695 (t) cc_final: 0.6879 (p) REVERT: H 64 GLN cc_start: 0.7398 (mp10) cc_final: 0.7020 (mt0) REVERT: H 139 ASP cc_start: 0.7642 (t0) cc_final: 0.7006 (p0) REVERT: H 190 GLU cc_start: 0.7594 (tt0) cc_final: 0.7333 (tt0) REVERT: H 425 ARG cc_start: 0.7480 (ttp-110) cc_final: 0.7116 (mtm-85) REVERT: L 43 ASP cc_start: 0.8510 (t70) cc_final: 0.8198 (t0) REVERT: L 48 ASP cc_start: 0.7560 (m-30) cc_final: 0.7315 (m-30) REVERT: L 51 SER cc_start: 0.7773 (t) cc_final: 0.6964 (p) REVERT: L 52 GLU cc_start: 0.7910 (mp0) cc_final: 0.7638 (mp0) REVERT: L 64 GLN cc_start: 0.7501 (mp10) cc_final: 0.6974 (mt0) REVERT: L 139 ASP cc_start: 0.7543 (t0) cc_final: 0.6927 (p0) REVERT: L 190 GLU cc_start: 0.7661 (tt0) cc_final: 0.7400 (tt0) REVERT: L 223 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7786 (tm) REVERT: L 298 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7967 (tm-30) REVERT: Q 51 SER cc_start: 0.7738 (t) cc_final: 0.6919 (p) REVERT: Q 64 GLN cc_start: 0.7488 (mp10) cc_final: 0.7012 (mt0) REVERT: Q 139 ASP cc_start: 0.7524 (t0) cc_final: 0.6919 (p0) REVERT: Q 190 GLU cc_start: 0.7471 (tt0) cc_final: 0.7193 (tt0) REVERT: Q 223 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7653 (tm) REVERT: Q 224 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.6258 (mp10) REVERT: R 421 MET cc_start: 0.7398 (mmm) cc_final: 0.6315 (mmm) outliers start: 65 outliers final: 45 residues processed: 319 average time/residue: 0.3354 time to fit residues: 157.7248 Evaluate side-chains 304 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 303 ASN Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain M residue 459 ARG Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Chi-restraints excluded: chain R residue 459 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN O 461 ASN D 185 GLN D 303 ASN H 303 ASN Q 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19680 Z= 0.271 Angle : 0.557 7.705 26630 Z= 0.292 Chirality : 0.046 0.223 2995 Planarity : 0.004 0.037 3260 Dihedral : 9.703 59.987 3561 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.53 % Allowed : 11.14 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.76 (0.17), residues: 2245 helix: 1.48 (0.21), residues: 615 sheet: 0.38 (0.19), residues: 665 loop : 0.09 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 241 HIS 0.002 0.001 HIS A 267 PHE 0.013 0.002 PHE A 98 TYR 0.029 0.002 TYR D 299 ARG 0.003 0.000 ARG O 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 265 time to evaluate : 2.066 Fit side-chains revert: symmetry clash REVERT: A 51 SER cc_start: 0.7587 (t) cc_final: 0.6867 (p) REVERT: A 64 GLN cc_start: 0.7430 (mp10) cc_final: 0.7023 (mt0) REVERT: A 139 ASP cc_start: 0.7389 (t0) cc_final: 0.6773 (p0) REVERT: A 190 GLU cc_start: 0.7525 (tt0) cc_final: 0.7200 (tt0) REVERT: A 223 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7886 (tm) REVERT: A 425 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.7219 (mtm-85) REVERT: O 421 MET cc_start: 0.7347 (mmm) cc_final: 0.6462 (mmm) REVERT: D 51 SER cc_start: 0.7522 (t) cc_final: 0.6795 (p) REVERT: D 64 GLN cc_start: 0.7450 (mp10) cc_final: 0.7000 (mt0) REVERT: D 139 ASP cc_start: 0.7521 (t0) cc_final: 0.6871 (p0) REVERT: D 190 GLU cc_start: 0.7475 (tt0) cc_final: 0.7142 (tt0) REVERT: D 223 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7789 (tm) REVERT: D 298 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7881 (tm-30) REVERT: D 303 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7782 (t0) REVERT: H 51 SER cc_start: 0.7677 (t) cc_final: 0.6855 (p) REVERT: H 64 GLN cc_start: 0.7396 (mp10) cc_final: 0.7045 (mt0) REVERT: H 139 ASP cc_start: 0.7617 (t0) cc_final: 0.6976 (p0) REVERT: H 190 GLU cc_start: 0.7600 (tt0) cc_final: 0.7318 (tt0) REVERT: H 298 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7884 (tm-30) REVERT: H 425 ARG cc_start: 0.7490 (ttp-110) cc_final: 0.7154 (mtm-85) REVERT: L 40 MET cc_start: 0.9003 (mtt) cc_final: 0.8702 (mtt) REVERT: L 43 ASP cc_start: 0.8477 (t70) cc_final: 0.8180 (t0) REVERT: L 48 ASP cc_start: 0.7512 (m-30) cc_final: 0.7256 (m-30) REVERT: L 51 SER cc_start: 0.7752 (t) cc_final: 0.6955 (p) REVERT: L 64 GLN cc_start: 0.7462 (mp10) cc_final: 0.6996 (mt0) REVERT: L 68 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7576 (ttm170) REVERT: L 139 ASP cc_start: 0.7532 (t0) cc_final: 0.6925 (p0) REVERT: L 190 GLU cc_start: 0.7668 (tt0) cc_final: 0.7407 (tt0) REVERT: L 223 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7845 (tm) REVERT: L 298 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7974 (tm-30) REVERT: M 470 MET cc_start: 0.3484 (mpp) cc_final: 0.3142 (mpp) REVERT: Q 51 SER cc_start: 0.7723 (t) cc_final: 0.6916 (p) REVERT: Q 64 GLN cc_start: 0.7452 (mp10) cc_final: 0.7018 (mt0) REVERT: Q 139 ASP cc_start: 0.7470 (t0) cc_final: 0.6913 (p0) REVERT: Q 190 GLU cc_start: 0.7508 (tt0) cc_final: 0.7211 (tt0) REVERT: Q 223 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7674 (tm) REVERT: Q 224 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6261 (mp10) REVERT: R 421 MET cc_start: 0.7340 (mmm) cc_final: 0.6270 (mmm) outliers start: 50 outliers final: 39 residues processed: 303 average time/residue: 0.3284 time to fit residues: 149.1810 Evaluate side-chains 299 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 254 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN D 303 ASN H 303 ASN L 185 GLN Q 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19680 Z= 0.229 Angle : 0.540 7.966 26630 Z= 0.282 Chirality : 0.045 0.234 2995 Planarity : 0.004 0.036 3260 Dihedral : 9.432 59.252 3561 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.53 % Allowed : 12.05 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.80 (0.18), residues: 2245 helix: 1.60 (0.21), residues: 615 sheet: 0.24 (0.19), residues: 695 loop : 0.19 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 168 HIS 0.003 0.001 HIS L 267 PHE 0.011 0.001 PHE A 98 TYR 0.029 0.002 TYR D 299 ARG 0.004 0.000 ARG L 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 268 time to evaluate : 1.929 Fit side-chains REVERT: A 51 SER cc_start: 0.7597 (t) cc_final: 0.6864 (p) REVERT: A 64 GLN cc_start: 0.7397 (mp10) cc_final: 0.6995 (mt0) REVERT: A 139 ASP cc_start: 0.7377 (t0) cc_final: 0.6785 (p0) REVERT: A 190 GLU cc_start: 0.7529 (tt0) cc_final: 0.7204 (tt0) REVERT: A 223 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7893 (tm) REVERT: A 298 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 425 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7175 (mtm-85) REVERT: D 51 SER cc_start: 0.7532 (t) cc_final: 0.6795 (p) REVERT: D 64 GLN cc_start: 0.7451 (mp10) cc_final: 0.7009 (mt0) REVERT: D 139 ASP cc_start: 0.7527 (t0) cc_final: 0.6866 (p0) REVERT: D 190 GLU cc_start: 0.7498 (tt0) cc_final: 0.7161 (tt0) REVERT: D 223 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7791 (tm) REVERT: D 298 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 303 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7730 (t0) REVERT: H 51 SER cc_start: 0.7670 (t) cc_final: 0.6859 (p) REVERT: H 64 GLN cc_start: 0.7393 (mp10) cc_final: 0.7028 (mt0) REVERT: H 190 GLU cc_start: 0.7651 (tt0) cc_final: 0.7401 (tt0) REVERT: H 298 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7905 (tm-30) REVERT: H 425 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.7138 (mtm-85) REVERT: L 40 MET cc_start: 0.9002 (mtt) cc_final: 0.8681 (mtt) REVERT: L 43 ASP cc_start: 0.8526 (t70) cc_final: 0.8213 (t0) REVERT: L 48 ASP cc_start: 0.7480 (m-30) cc_final: 0.7193 (m-30) REVERT: L 51 SER cc_start: 0.7752 (t) cc_final: 0.6947 (p) REVERT: L 64 GLN cc_start: 0.7447 (mp10) cc_final: 0.6993 (mt0) REVERT: L 139 ASP cc_start: 0.7516 (t0) cc_final: 0.6921 (p0) REVERT: L 190 GLU cc_start: 0.7676 (tt0) cc_final: 0.7414 (tt0) REVERT: L 223 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7858 (tm) REVERT: L 298 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7977 (tm-30) REVERT: M 470 MET cc_start: 0.3661 (mpp) cc_final: 0.3322 (mpp) REVERT: Q 51 SER cc_start: 0.7739 (t) cc_final: 0.6929 (p) REVERT: Q 64 GLN cc_start: 0.7354 (mp10) cc_final: 0.6955 (mt0) REVERT: Q 139 ASP cc_start: 0.7447 (t0) cc_final: 0.6931 (p0) REVERT: Q 190 GLU cc_start: 0.7557 (tt0) cc_final: 0.7285 (tt0) REVERT: Q 223 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7665 (tm) REVERT: Q 224 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6230 (mp10) REVERT: R 421 MET cc_start: 0.7345 (mmm) cc_final: 0.6322 (mmm) outliers start: 50 outliers final: 37 residues processed: 306 average time/residue: 0.3242 time to fit residues: 147.6320 Evaluate side-chains 301 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 258 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 137 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN D 303 ASN H 303 ASN L 185 GLN M 461 ASN Q 185 GLN R 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 19680 Z= 0.552 Angle : 0.705 7.000 26630 Z= 0.369 Chirality : 0.051 0.236 2995 Planarity : 0.005 0.039 3260 Dihedral : 10.408 62.652 3561 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.84 % Allowed : 12.61 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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 (0.17), residues: 2245 helix: 0.45 (0.20), residues: 650 sheet: -0.06 (0.18), residues: 715 loop : -0.18 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 440 HIS 0.004 0.001 HIS H 107 PHE 0.018 0.002 PHE L 306 TYR 0.029 0.003 TYR Q 66 ARG 0.004 0.001 ARG Q 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 262 time to evaluate : 1.871 Fit side-chains REVERT: A 51 SER cc_start: 0.7762 (t) cc_final: 0.7003 (p) REVERT: A 139 ASP cc_start: 0.7443 (t0) cc_final: 0.6875 (p0) REVERT: A 190 GLU cc_start: 0.7503 (tt0) cc_final: 0.7091 (tt0) REVERT: A 425 ARG cc_start: 0.7502 (ttp-170) cc_final: 0.7216 (mtm-85) REVERT: O 421 MET cc_start: 0.7197 (mmm) cc_final: 0.6332 (mmm) REVERT: D 51 SER cc_start: 0.7614 (t) cc_final: 0.6898 (p) REVERT: D 64 GLN cc_start: 0.7675 (mp10) cc_final: 0.7068 (mt0) REVERT: D 139 ASP cc_start: 0.7497 (t0) cc_final: 0.6868 (p0) REVERT: D 190 GLU cc_start: 0.7434 (tt0) cc_final: 0.7107 (tt0) REVERT: D 223 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7743 (tm) REVERT: D 298 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7839 (tm-30) REVERT: H 51 SER cc_start: 0.7742 (t) cc_final: 0.6928 (p) REVERT: H 64 GLN cc_start: 0.7509 (mp10) cc_final: 0.6957 (mt0) REVERT: H 139 ASP cc_start: 0.7592 (t0) cc_final: 0.7010 (p0) REVERT: H 190 GLU cc_start: 0.7610 (tt0) cc_final: 0.7355 (tt0) REVERT: H 298 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7814 (tm-30) REVERT: H 425 ARG cc_start: 0.7499 (ttp-110) cc_final: 0.7168 (mtm-85) REVERT: L 40 MET cc_start: 0.8958 (mtt) cc_final: 0.8723 (mtt) REVERT: L 43 ASP cc_start: 0.8568 (t70) cc_final: 0.8350 (t0) REVERT: L 48 ASP cc_start: 0.7659 (m-30) cc_final: 0.7436 (m-30) REVERT: L 51 SER cc_start: 0.7696 (t) cc_final: 0.6892 (p) REVERT: L 139 ASP cc_start: 0.7504 (t0) cc_final: 0.6940 (p0) REVERT: L 190 GLU cc_start: 0.7673 (tt0) cc_final: 0.7392 (tt0) REVERT: L 223 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7762 (tm) REVERT: M 421 MET cc_start: 0.7148 (mmm) cc_final: 0.6263 (mmm) REVERT: Q 51 SER cc_start: 0.7748 (t) cc_final: 0.6965 (p) REVERT: Q 55 MET cc_start: 0.7749 (mtp) cc_final: 0.7533 (mtp) REVERT: Q 64 GLN cc_start: 0.7585 (mp10) cc_final: 0.6990 (mt0) REVERT: Q 139 ASP cc_start: 0.7506 (t0) cc_final: 0.6979 (p0) REVERT: Q 190 GLU cc_start: 0.7465 (tt0) cc_final: 0.7128 (tt0) REVERT: Q 223 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7496 (tm) REVERT: Q 224 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.6196 (mp10) REVERT: R 421 MET cc_start: 0.7157 (mmm) cc_final: 0.6234 (mmm) outliers start: 56 outliers final: 41 residues processed: 307 average time/residue: 0.3318 time to fit residues: 151.8185 Evaluate side-chains 298 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 253 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 309 GLN Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 0.5980 chunk 189 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 182 optimal weight: 0.1980 chunk 191 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 132 optimal weight: 40.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 185 GLN D 303 ASN H 303 ASN Q 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19680 Z= 0.141 Angle : 0.530 8.534 26630 Z= 0.276 Chirality : 0.044 0.241 2995 Planarity : 0.004 0.038 3260 Dihedral : 8.989 58.561 3561 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.77 % Allowed : 14.23 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.59 (0.18), residues: 2245 helix: 1.25 (0.21), residues: 645 sheet: 0.31 (0.19), residues: 695 loop : -0.02 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 423 HIS 0.003 0.001 HIS D 191 PHE 0.008 0.001 PHE A 98 TYR 0.029 0.001 TYR L 446 ARG 0.004 0.000 ARG L 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 279 time to evaluate : 2.146 Fit side-chains REVERT: A 51 SER cc_start: 0.7574 (t) cc_final: 0.6810 (p) REVERT: A 64 GLN cc_start: 0.7432 (mp10) cc_final: 0.7023 (mt0) REVERT: A 66 TYR cc_start: 0.7903 (m-80) cc_final: 0.7680 (m-80) REVERT: A 139 ASP cc_start: 0.7382 (t0) cc_final: 0.6849 (p0) REVERT: A 148 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7391 (mm110) REVERT: A 190 GLU cc_start: 0.7502 (tt0) cc_final: 0.7169 (tt0) REVERT: A 223 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7876 (tm) REVERT: A 298 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 425 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7180 (mtm-85) REVERT: O 421 MET cc_start: 0.7239 (mmm) cc_final: 0.6581 (mmm) REVERT: D 51 SER cc_start: 0.7562 (t) cc_final: 0.6802 (p) REVERT: D 64 GLN cc_start: 0.7409 (mp10) cc_final: 0.6927 (mt0) REVERT: D 139 ASP cc_start: 0.7500 (t0) cc_final: 0.6869 (p0) REVERT: D 148 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7392 (mm-40) REVERT: D 190 GLU cc_start: 0.7511 (tt0) cc_final: 0.7178 (tt0) REVERT: D 223 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7768 (tm) REVERT: D 298 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7774 (tm-30) REVERT: H 40 MET cc_start: 0.9016 (mtt) cc_final: 0.8399 (mtt) REVERT: H 51 SER cc_start: 0.7674 (t) cc_final: 0.6838 (p) REVERT: H 64 GLN cc_start: 0.7399 (mp10) cc_final: 0.7035 (mt0) REVERT: H 139 ASP cc_start: 0.7497 (t0) cc_final: 0.6917 (p0) REVERT: H 190 GLU cc_start: 0.7602 (tt0) cc_final: 0.7326 (tt0) REVERT: H 298 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7921 (tm-30) REVERT: H 425 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.7180 (mtm-85) REVERT: I 470 MET cc_start: 0.3353 (mpp) cc_final: 0.2992 (mpp) REVERT: L 40 MET cc_start: 0.9018 (mtt) cc_final: 0.8658 (mtt) REVERT: L 41 ASN cc_start: 0.8333 (m110) cc_final: 0.7779 (m110) REVERT: L 43 ASP cc_start: 0.8507 (t70) cc_final: 0.8194 (t0) REVERT: L 48 ASP cc_start: 0.7477 (m-30) cc_final: 0.7175 (m-30) REVERT: L 51 SER cc_start: 0.7656 (t) cc_final: 0.6835 (p) REVERT: L 64 GLN cc_start: 0.7431 (mp10) cc_final: 0.6864 (mt0) REVERT: L 139 ASP cc_start: 0.7453 (t0) cc_final: 0.6932 (p0) REVERT: L 190 GLU cc_start: 0.7662 (tt0) cc_final: 0.7384 (tt0) REVERT: L 223 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7868 (tm) REVERT: L 235 LEU cc_start: 0.8396 (tp) cc_final: 0.8182 (tt) REVERT: L 298 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7885 (tm-30) REVERT: M 421 MET cc_start: 0.7363 (mmm) cc_final: 0.6450 (mmm) REVERT: Q 12 VAL cc_start: 0.8314 (t) cc_final: 0.8102 (m) REVERT: Q 51 SER cc_start: 0.7733 (t) cc_final: 0.6921 (p) REVERT: Q 64 GLN cc_start: 0.7362 (mp10) cc_final: 0.6809 (mt0) REVERT: Q 139 ASP cc_start: 0.7405 (t0) cc_final: 0.6920 (p0) REVERT: Q 190 GLU cc_start: 0.7565 (tt0) cc_final: 0.7302 (tt0) REVERT: Q 223 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7622 (tm) REVERT: Q 224 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.6158 (mp10) REVERT: Q 298 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7884 (tm-30) REVERT: R 421 MET cc_start: 0.7247 (mmm) cc_final: 0.6577 (mmm) REVERT: R 496 PRO cc_start: 0.6346 (Cg_endo) cc_final: 0.6098 (Cg_exo) outliers start: 35 outliers final: 26 residues processed: 303 average time/residue: 0.3234 time to fit residues: 148.1373 Evaluate side-chains 298 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 267 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 137 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN D 303 ASN H 303 ASN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19680 Z= 0.165 Angle : 0.523 8.080 26630 Z= 0.272 Chirality : 0.044 0.246 2995 Planarity : 0.004 0.037 3260 Dihedral : 8.364 59.340 3561 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.77 % Allowed : 14.63 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.70 (0.18), residues: 2245 helix: 1.28 (0.21), residues: 645 sheet: 0.47 (0.19), residues: 695 loop : -0.00 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 423 HIS 0.003 0.001 HIS H 191 PHE 0.021 0.001 PHE Q 301 TYR 0.029 0.002 TYR L 299 ARG 0.004 0.000 ARG D 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4490 Ramachandran restraints generated. 2245 Oldfield, 0 Emsley, 2245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 283 time to evaluate : 1.982 Fit side-chains REVERT: A 51 SER cc_start: 0.7625 (t) cc_final: 0.6846 (p) REVERT: A 64 GLN cc_start: 0.7420 (mp10) cc_final: 0.7029 (mt0) REVERT: A 139 ASP cc_start: 0.7382 (t0) cc_final: 0.6860 (p0) REVERT: A 148 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7396 (mm110) REVERT: A 190 GLU cc_start: 0.7555 (tt0) cc_final: 0.7222 (tt0) REVERT: A 223 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7862 (tm) REVERT: A 298 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 425 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.7120 (mtm-85) REVERT: O 421 MET cc_start: 0.7181 (mmm) cc_final: 0.6599 (mmm) REVERT: D 51 SER cc_start: 0.7613 (t) cc_final: 0.6870 (p) REVERT: D 64 GLN cc_start: 0.7428 (mp10) cc_final: 0.6998 (mt0) REVERT: D 139 ASP cc_start: 0.7487 (t0) cc_final: 0.6888 (p0) REVERT: D 190 GLU cc_start: 0.7529 (tt0) cc_final: 0.7189 (tt0) REVERT: D 223 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7766 (tm) REVERT: D 298 GLU cc_start: 0.8260 (tm-30) cc_final: 0.8015 (tm-30) REVERT: H 51 SER cc_start: 0.7702 (t) cc_final: 0.6908 (p) REVERT: H 64 GLN cc_start: 0.7358 (mp10) cc_final: 0.6997 (mt0) REVERT: H 139 ASP cc_start: 0.7542 (t0) cc_final: 0.6978 (p0) REVERT: H 147 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6219 (mm-30) REVERT: H 190 GLU cc_start: 0.7653 (tt0) cc_final: 0.7392 (tt0) REVERT: H 298 GLU cc_start: 0.8242 (tm-30) cc_final: 0.8024 (tm-30) REVERT: H 425 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7139 (mtm-85) REVERT: L 40 MET cc_start: 0.8989 (mtt) cc_final: 0.8395 (mtt) REVERT: L 41 ASN cc_start: 0.8318 (m110) cc_final: 0.7802 (m110) REVERT: L 43 ASP cc_start: 0.8464 (t70) cc_final: 0.8134 (t0) REVERT: L 51 SER cc_start: 0.7689 (t) cc_final: 0.6869 (p) REVERT: L 64 GLN cc_start: 0.7412 (mp10) cc_final: 0.6946 (mt0) REVERT: L 139 ASP cc_start: 0.7408 (t0) cc_final: 0.6909 (p0) REVERT: L 190 GLU cc_start: 0.7702 (tt0) cc_final: 0.7436 (tt0) REVERT: L 298 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7977 (tm-30) REVERT: M 421 MET cc_start: 0.7346 (mmm) cc_final: 0.6459 (mmm) REVERT: Q 12 VAL cc_start: 0.8269 (t) cc_final: 0.8043 (m) REVERT: Q 51 SER cc_start: 0.7808 (t) cc_final: 0.7020 (p) REVERT: Q 64 GLN cc_start: 0.7228 (mp10) cc_final: 0.6887 (mt0) REVERT: Q 139 ASP cc_start: 0.7392 (t0) cc_final: 0.6921 (p0) REVERT: Q 190 GLU cc_start: 0.7626 (tt0) cc_final: 0.7353 (tt0) REVERT: Q 223 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7633 (tm) REVERT: Q 224 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.5944 (mp10) REVERT: R 421 MET cc_start: 0.7280 (mmm) cc_final: 0.6614 (mmm) REVERT: R 496 PRO cc_start: 0.6316 (Cg_endo) cc_final: 0.6071 (Cg_exo) outliers start: 35 outliers final: 27 residues processed: 309 average time/residue: 0.3187 time to fit residues: 147.8430 Evaluate side-chains 298 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 267 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 271 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 423 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain Q residue 132 THR Chi-restraints excluded: chain Q residue 176 THR Chi-restraints excluded: chain Q residue 223 LEU Chi-restraints excluded: chain Q residue 224 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 26 optimal weight: 0.0050 chunk 49 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.145482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.103960 restraints weight = 23451.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.101617 restraints weight = 37360.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.103434 restraints weight = 35423.920| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19680 Z= 0.228 Angle : 0.549 8.093 26630 Z= 0.285 Chirality : 0.045 0.251 2995 Planarity : 0.004 0.037 3260 Dihedral : 8.305 59.944 3559 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.77 % Allowed : 15.04 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.62 (0.18), residues: 2245 helix: 1.14 (0.21), residues: 645 sheet: 0.47 (0.19), residues: 695 loop : -0.02 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 440 HIS 0.003 0.001 HIS H 191 PHE 0.016 0.001 PHE Q 301 TYR 0.028 0.002 TYR L 299 ARG 0.004 0.000 ARG D 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.23 seconds wall clock time: 69 minutes 0.13 seconds (4140.13 seconds total)