Starting phenix.real_space_refine on Mon Dec 11 21:42:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_17960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_17960.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_17960_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_17960_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_17960_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_17960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_17960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_17960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvb_17960/12_2023/8pvb_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 6 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: 6 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: 6 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: 6 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: 10.12, per 1000 atoms: 0.53 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: 7.57 Conformation dependent library (CDL) restraints added in 3.5 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: 4.00 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: 6.78 Time building geometry restraints manager: 8.18 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 - 17.97: 10515 17.97 - 35.95: 895 35.95 - 53.92: 150 53.92 - 71.90: 75 71.90 - 89.87: 25 Dihedral angle restraints: 11660 sinusoidal: 5010 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 11657 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: 1.290 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: 7.430 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 53.290 Find NCS groups from input model: 1.260 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.770 ------------------------------------------------------------------------------- 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 : 0.011 0.065 19680 Z= 0.681 Angle : 1.705 9.123 26630 Z= 1.129 Chirality : 0.086 0.274 2995 Planarity : 0.012 0.135 3260 Dihedral : 14.678 89.871 7415 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 : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 426 average time/residue: 0.3566 time to fit residues: 220.1442 Evaluate side-chains 290 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 274 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.3570 time to fit residues: 10.9944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 176 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 148 GLN A 185 GLN D 41 ASN D 185 GLN H 41 ASN H 185 GLN L 185 GLN Q 41 ASN Q 185 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2050 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= 0.175 Angle : 0.598 7.073 26630 Z= 0.319 Chirality : 0.045 0.175 2995 Planarity : 0.004 0.036 3260 Dihedral : 7.878 55.477 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.22 % Allowed : 8.15 % Favored : 90.63 % 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: 1.04 (0.18), residues: 2245 helix: 1.45 (0.20), residues: 610 sheet: 0.49 (0.19), residues: 685 loop : 0.52 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 443 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 D 213 *********************** 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 315 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 291 time to evaluate : 2.177 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 310 average time/residue: 0.3561 time to fit residues: 162.7869 Evaluate side-chains 267 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1737 time to fit residues: 7.8491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 182 optimal weight: 0.1980 chunk 202 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 164 optimal weight: 0.0470 overall best weight: 1.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 185 GLN O 461 ASN D 41 ASN D 64 GLN D 185 GLN E 461 ASN H 41 ASN H 64 GLN I 461 ASN L 64 GLN M 461 ASN Q 41 ASN Q 185 GLN R 461 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19680 Z= 0.235 Angle : 0.559 6.990 26630 Z= 0.299 Chirality : 0.045 0.157 2995 Planarity : 0.004 0.036 3260 Dihedral : 7.304 59.849 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.32 % Allowed : 9.62 % Favored : 89.06 % 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: 1.23 (0.18), residues: 2245 helix: 1.65 (0.20), residues: 615 sheet: 0.63 (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 0.003 0.001 HIS Q 267 PHE 0.016 0.002 PHE O 424 TYR 0.029 0.002 TYR D 299 ARG 0.003 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 304 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 278 time to evaluate : 2.138 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 294 average time/residue: 0.3519 time to fit residues: 153.7800 Evaluate side-chains 259 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 245 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1808 time to fit residues: 7.4064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 205 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 64 GLN D 185 GLN H 41 ASN L 64 GLN Q 41 ASN Q 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19680 Z= 0.162 Angle : 0.506 6.648 26630 Z= 0.269 Chirality : 0.043 0.163 2995 Planarity : 0.004 0.035 3260 Dihedral : 6.868 56.855 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.35 % Allowed : 11.09 % Favored : 88.56 % 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: 1.28 (0.18), residues: 2245 helix: 1.87 (0.20), residues: 615 sheet: 0.52 (0.19), residues: 695 loop : 0.60 (0.22), residues: 935 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 0.016 0.001 PHE E 424 TYR 0.030 0.001 TYR D 299 ARG 0.006 0.000 ARG D 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 281 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 274 time to evaluate : 1.937 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 276 average time/residue: 0.3509 time to fit residues: 142.7005 Evaluate side-chains 256 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 250 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1661 time to fit residues: 4.5268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 chunk 161 optimal weight: 0.0970 chunk 89 optimal weight: 0.0980 chunk 185 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 185 GLN D 185 GLN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2936 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= 0.169 Angle : 0.498 7.081 26630 Z= 0.265 Chirality : 0.043 0.154 2995 Planarity : 0.004 0.034 3260 Dihedral : 6.594 59.710 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.51 % Allowed : 11.59 % Favored : 87.90 % 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: 1.31 (0.18), residues: 2245 helix: 1.94 (0.21), residues: 615 sheet: 0.56 (0.19), residues: 690 loop : 0.54 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 67 HIS 0.002 0.001 HIS H 191 PHE 0.012 0.001 PHE M 424 TYR 0.028 0.001 TYR H 299 ARG 0.007 0.000 ARG D 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 284 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 274 time to evaluate : 2.134 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 278 average time/residue: 0.3599 time to fit residues: 147.9921 Evaluate side-chains 265 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1978 time to fit residues: 4.9139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 185 GLN D 185 GLN L 185 GLN Q 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 19680 Z= 0.435 Angle : 0.644 6.263 26630 Z= 0.339 Chirality : 0.048 0.174 2995 Planarity : 0.005 0.043 3260 Dihedral : 8.145 59.257 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.22 % Allowed : 12.51 % Favored : 86.28 % 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: 0.36 (0.18), residues: 2245 helix: 0.88 (0.20), residues: 645 sheet: 0.01 (0.18), residues: 740 loop : 0.18 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 440 HIS 0.004 0.001 HIS A 267 PHE 0.017 0.002 PHE H 98 TYR 0.034 0.003 TYR Q 66 ARG 0.008 0.001 ARG D 213 *********************** 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 276 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 2.009 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 270 average time/residue: 0.3523 time to fit residues: 141.7298 Evaluate side-chains 255 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 241 time to evaluate : 2.119 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1784 time to fit residues: 7.8706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 124 optimal weight: 20.0000 chunk 158 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 L 41 ASN Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3270 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= 0.213 Angle : 0.529 6.653 26630 Z= 0.281 Chirality : 0.043 0.191 2995 Planarity : 0.004 0.037 3260 Dihedral : 7.526 59.484 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.41 % Allowed : 14.23 % Favored : 85.37 % 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: 0.82 (0.18), residues: 2245 helix: 1.57 (0.21), residues: 615 sheet: 0.23 (0.19), residues: 710 loop : 0.27 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 440 HIS 0.003 0.001 HIS Q 191 PHE 0.014 0.001 PHE L 98 TYR 0.030 0.002 TYR Q 66 ARG 0.007 0.000 ARG D 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 272 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 2.184 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 269 average time/residue: 0.3683 time to fit residues: 147.6337 Evaluate side-chains 259 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 254 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1836 time to fit residues: 4.6679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0020 chunk 129 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 137 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 overall best weight: 1.9194 ------------------------------------------------------------------------------- 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 Q 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 19680 Z= 0.299 Angle : 0.568 6.825 26630 Z= 0.302 Chirality : 0.045 0.190 2995 Planarity : 0.004 0.037 3260 Dihedral : 7.427 59.999 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.66 % Allowed : 14.08 % Favored : 85.27 % 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: 0.46 (0.18), residues: 2245 helix: 1.09 (0.21), residues: 645 sheet: 0.03 (0.18), residues: 740 loop : 0.17 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 440 HIS 0.002 0.001 HIS Q 191 PHE 0.017 0.002 PHE D 301 TYR 0.035 0.002 TYR Q 66 ARG 0.007 0.000 ARG D 213 *********************** 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 273 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 260 time to evaluate : 2.267 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 268 average time/residue: 0.3657 time to fit residues: 145.9448 Evaluate side-chains 258 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 250 time to evaluate : 2.091 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1836 time to fit residues: 5.5863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 121 optimal weight: 0.3980 chunk 88 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 182 optimal weight: 0.0030 chunk 191 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 overall best weight: 0.4348 ------------------------------------------------------------------------------- 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 Q 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19680 Z= 0.130 Angle : 0.497 7.675 26630 Z= 0.263 Chirality : 0.042 0.174 2995 Planarity : 0.003 0.037 3260 Dihedral : 6.711 58.922 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.10 % Allowed : 14.48 % 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: 1.07 (0.18), residues: 2245 helix: 1.85 (0.21), residues: 615 sheet: 0.41 (0.19), residues: 710 loop : 0.32 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 440 HIS 0.003 0.001 HIS Q 191 PHE 0.015 0.001 PHE D 301 TYR 0.031 0.001 TYR Q 66 ARG 0.007 0.000 ARG D 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 286 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.3365 time to fit residues: 143.9342 Evaluate side-chains 261 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1832 time to fit residues: 3.4500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 206 optimal weight: 0.2980 chunk 178 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.0870 chunk 109 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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: 0.7581 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19680 Z= 0.172 Angle : 0.515 7.578 26630 Z= 0.271 Chirality : 0.043 0.193 2995 Planarity : 0.004 0.036 3260 Dihedral : 6.538 59.623 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.10 % Allowed : 15.14 % Favored : 84.76 % 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: 1.02 (0.18), residues: 2245 helix: 1.77 (0.21), residues: 615 sheet: 0.45 (0.19), residues: 720 loop : 0.26 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 440 HIS 0.003 0.001 HIS H 191 PHE 0.017 0.001 PHE A 301 TYR 0.029 0.002 TYR Q 66 ARG 0.007 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 276 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 2.195 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 275 average time/residue: 0.3533 time to fit residues: 144.5861 Evaluate side-chains 265 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2139 time to fit residues: 3.0402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 26 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 185 GLN Q 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.149020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110763 restraints weight = 23222.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.109413 restraints weight = 39138.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.109453 restraints weight = 36671.733| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19680 Z= 0.138 Angle : 0.497 7.710 26630 Z= 0.262 Chirality : 0.042 0.181 2995 Planarity : 0.003 0.036 3260 Dihedral : 6.152 56.426 3255 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.00 % Allowed : 15.34 % Favored : 84.66 % 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: 1.21 (0.18), residues: 2245 helix: 1.96 (0.21), residues: 615 sheet: 0.72 (0.19), residues: 690 loop : 0.20 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 440 HIS 0.003 0.001 HIS H 191 PHE 0.017 0.001 PHE A 301 TYR 0.028 0.001 TYR Q 66 ARG 0.007 0.000 ARG D 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3879.12 seconds wall clock time: 71 minutes 40.93 seconds (4300.93 seconds total)