Starting phenix.real_space_refine on Fri Feb 16 01:38:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxd_20518/02_2024/6pxd_20518_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxd_20518/02_2024/6pxd_20518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxd_20518/02_2024/6pxd_20518.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxd_20518/02_2024/6pxd_20518.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxd_20518/02_2024/6pxd_20518_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pxd_20518/02_2024/6pxd_20518_neut.pdb" } resolution = 2.9 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= 0.003 sd= 0.052 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 90 5.16 5 Cl 3 4.86 5 C 9055 2.51 5 N 2255 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 212": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13899 Number of models: 1 Model: "" Number of chains: 13 Chain: "E" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "A" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "B" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "C" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 Chain: "D" Number of atoms: 2751 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 340, 2740 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 324} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2797 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: 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: "H" 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: "I" 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: "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: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG E 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 75 " occ=0.50 residue: pdb=" N AARG A 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 75 " occ=0.50 residue: pdb=" N AARG B 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 75 " occ=0.50 residue: pdb=" N AARG C 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 75 " occ=0.50 residue: pdb=" N AARG D 75 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 75 " occ=0.50 Time building chain proxies: 13.07, per 1000 atoms: 0.94 Number of scatterers: 13899 At special positions: 0 Unit cell: (97.76, 99.84, 132.08, 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 3 17.00 S 90 16.00 O 2496 8.00 N 2255 7.00 C 9055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN E 54 " " NAG G 1 " - " ASN A 54 " " NAG H 1 " - " ASN B 54 " " NAG I 1 " - " ASN C 54 " " NAG J 1 " - " ASN D 54 " Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 4.6 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 25 sheets defined 38.2% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.565A pdb=" N ALA E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 102 through 109 removed outlier: 3.885A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 109 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 removed outlier: 4.519A pdb=" N ASN E 160 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.892A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 286 Processing helix chain 'E' and resid 297 through 324 removed outlier: 3.655A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 363 removed outlier: 3.916A pdb=" N VAL E 344 " --> pdb=" O THR E 340 " (cutoff:3.500A) Proline residue: E 347 - end of helix removed outlier: 3.662A pdb=" N TRP E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.564A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.884A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 4.518A pdb=" N ASN A 160 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.893A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 286 Processing helix chain 'A' and resid 297 through 324 removed outlier: 3.655A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 363 removed outlier: 3.917A pdb=" N VAL A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.663A pdb=" N TRP A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 87 through 90 removed outlier: 3.566A pdb=" N ALA B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.885A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 109 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 4.519A pdb=" N ASN B 160 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.893A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 286 Processing helix chain 'B' and resid 297 through 324 removed outlier: 3.655A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 363 removed outlier: 3.917A pdb=" N VAL B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.661A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 87 through 90 removed outlier: 3.565A pdb=" N ALA C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.885A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 109 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 4.519A pdb=" N ASN C 160 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.892A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 286 Processing helix chain 'C' and resid 297 through 324 removed outlier: 3.655A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 363 removed outlier: 3.917A pdb=" N VAL C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Proline residue: C 347 - end of helix removed outlier: 3.663A pdb=" N TRP C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.565A pdb=" N ALA D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 102 through 109 removed outlier: 3.885A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 removed outlier: 4.519A pdb=" N ASN D 160 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 removed outlier: 3.630A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.892A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 Processing helix chain 'D' and resid 297 through 324 removed outlier: 3.656A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 363 removed outlier: 3.917A pdb=" N VAL D 344 " --> pdb=" O THR D 340 " (cutoff:3.500A) Proline residue: D 347 - end of helix removed outlier: 3.663A pdb=" N TRP D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 99 through 101 removed outlier: 4.242A pdb=" N LEU E 134 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N AARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE E 64 " --> pdb=" O AARG E 75 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 119 through 123 removed outlier: 6.345A pdb=" N VAL E 151 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA E 122 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 149 " --> pdb=" O ALA E 122 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N AARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE E 64 " --> pdb=" O AARG E 75 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'E' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.241A pdb=" N LEU A 134 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 64 " --> pdb=" O AARG A 75 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 119 through 123 removed outlier: 6.344A pdb=" N VAL A 151 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 122 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 149 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 64 " --> pdb=" O AARG A 75 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.242A pdb=" N LEU B 134 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 64 " --> pdb=" O AARG B 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.344A pdb=" N VAL B 151 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA B 122 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 149 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 64 " --> pdb=" O AARG B 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.242A pdb=" N LEU C 134 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C 64 " --> pdb=" O AARG C 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 119 through 123 removed outlier: 6.345A pdb=" N VAL C 151 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA C 122 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 149 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N AARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C 64 " --> pdb=" O AARG C 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.242A pdb=" N LEU D 134 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N AARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE D 64 " --> pdb=" O AARG D 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 119 through 123 removed outlier: 6.344A pdb=" N VAL D 151 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA D 122 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 149 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N AARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE D 64 " --> pdb=" O AARG D 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'D' and resid 216 through 217 805 hydrogen bonds defined for protein. 2335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4285 1.35 - 1.47: 3752 1.47 - 1.60: 6058 1.60 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 14245 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.55e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 ... (remaining 14240 not shown) Histogram of bond angle deviations from ideal: 97.54 - 104.83: 277 104.83 - 112.13: 6804 112.13 - 119.42: 4780 119.42 - 126.72: 7260 126.72 - 134.01: 224 Bond angle restraints: 19345 Sorted by residual: angle pdb=" N ALA B 345 " pdb=" CA ALA B 345 " pdb=" C ALA B 345 " ideal model delta sigma weight residual 111.28 121.40 -10.12 1.09e+00 8.42e-01 8.62e+01 angle pdb=" N ALA A 345 " pdb=" CA ALA A 345 " pdb=" C ALA A 345 " ideal model delta sigma weight residual 111.28 121.39 -10.11 1.09e+00 8.42e-01 8.60e+01 angle pdb=" N ALA D 345 " pdb=" CA ALA D 345 " pdb=" C ALA D 345 " ideal model delta sigma weight residual 111.28 121.38 -10.10 1.09e+00 8.42e-01 8.58e+01 angle pdb=" N ALA E 345 " pdb=" CA ALA E 345 " pdb=" C ALA E 345 " ideal model delta sigma weight residual 111.28 121.37 -10.09 1.09e+00 8.42e-01 8.58e+01 angle pdb=" N ALA C 345 " pdb=" CA ALA C 345 " pdb=" C ALA C 345 " ideal model delta sigma weight residual 111.28 121.37 -10.09 1.09e+00 8.42e-01 8.56e+01 ... (remaining 19340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 8173 15.77 - 31.53: 312 31.53 - 47.30: 105 47.30 - 63.06: 30 63.06 - 78.83: 10 Dihedral angle restraints: 8630 sinusoidal: 3590 harmonic: 5040 Sorted by residual: dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.83 78.83 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.83 78.83 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -164.82 78.82 1 1.00e+01 1.00e-02 7.74e+01 ... (remaining 8627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2015 0.096 - 0.192: 175 0.192 - 0.287: 0 0.287 - 0.383: 10 0.383 - 0.479: 5 Chirality restraints: 2205 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 54 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 54 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D 54 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 2202 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C THR B 128 " -0.044 2.00e-02 2.50e+03 pdb=" O THR B 128 " 0.016 2.00e-02 2.50e+03 pdb=" N THR B 129 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 128 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR A 128 " -0.044 2.00e-02 2.50e+03 pdb=" O THR A 128 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 129 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 128 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C THR D 128 " 0.044 2.00e-02 2.50e+03 pdb=" O THR D 128 " -0.016 2.00e-02 2.50e+03 pdb=" N THR D 129 " -0.015 2.00e-02 2.50e+03 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 395 2.70 - 3.25: 12981 3.25 - 3.80: 21915 3.80 - 4.35: 28725 4.35 - 4.90: 49609 Nonbonded interactions: 113625 Sorted by model distance: nonbonded pdb=" OD2 ASP E 41 " pdb=" OG SER A 27 " model vdw 2.154 2.440 nonbonded pdb=" OD2 ASP B 41 " pdb=" OG SER C 27 " model vdw 2.192 2.440 nonbonded pdb=" OD2 ASP C 41 " pdb=" OG SER D 27 " model vdw 2.195 2.440 nonbonded pdb=" O LEU C 106 " pdb=" NZ LYS C 111 " model vdw 2.233 2.520 nonbonded pdb=" O LEU E 106 " pdb=" NZ LYS E 111 " model vdw 2.233 2.520 ... (remaining 113620 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' and (resid 25 through 74 or resid 76 through 364)) selection = (chain 'B' and (resid 25 through 74 or resid 76 through 364)) selection = (chain 'C' and (resid 25 through 74 or resid 76 through 364)) selection = (chain 'D' and (resid 25 through 74 or resid 76 through 364)) selection = (chain 'E' and (resid 25 through 74 or resid 76 through 364)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 5.130 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 45.750 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.007 0.060 14245 Z= 0.439 Angle : 1.047 11.033 19345 Z= 0.619 Chirality : 0.062 0.479 2205 Planarity : 0.008 0.062 2410 Dihedral : 10.489 70.313 5340 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.32 % Allowed : 2.65 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % 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: -3.03 (0.17), residues: 1705 helix: -2.32 (0.17), residues: 545 sheet: -0.84 (0.26), residues: 380 loop : -2.31 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP C 110 HIS 0.004 0.001 HIS A 231 PHE 0.029 0.003 PHE C 116 TYR 0.023 0.003 TYR C 144 ARG 0.007 0.001 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 357 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: E 96 ASP cc_start: 0.6338 (p0) cc_final: 0.5993 (p0) REVERT: E 107 ASP cc_start: 0.8157 (m-30) cc_final: 0.7875 (m-30) REVERT: E 159 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8180 (mmtt) REVERT: E 189 LYS cc_start: 0.8387 (tptp) cc_final: 0.8166 (tppp) REVERT: E 210 ASP cc_start: 0.7446 (t70) cc_final: 0.6987 (t70) REVERT: E 222 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8628 (mtmt) REVERT: E 279 MET cc_start: 0.8520 (tpp) cc_final: 0.8305 (tpt) REVERT: E 287 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7193 (mtt-85) REVERT: E 339 ASP cc_start: 0.5828 (t0) cc_final: 0.5478 (t0) REVERT: A 96 ASP cc_start: 0.6038 (p0) cc_final: 0.5812 (p0) REVERT: A 105 MET cc_start: 0.8006 (mmm) cc_final: 0.7710 (mmm) REVERT: A 107 ASP cc_start: 0.8073 (m-30) cc_final: 0.7857 (m-30) REVERT: A 159 LYS cc_start: 0.8575 (tmmt) cc_final: 0.8107 (mttm) REVERT: A 185 GLU cc_start: 0.7954 (pt0) cc_final: 0.7713 (mt-10) REVERT: A 227 GLU cc_start: 0.8322 (pt0) cc_final: 0.8118 (pt0) REVERT: A 279 MET cc_start: 0.8582 (tpp) cc_final: 0.8377 (tpt) REVERT: A 337 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.4921 (mtt180) REVERT: A 339 ASP cc_start: 0.5903 (t0) cc_final: 0.5615 (t0) REVERT: A 350 PHE cc_start: 0.8131 (t80) cc_final: 0.7552 (t80) REVERT: B 210 ASP cc_start: 0.7448 (t70) cc_final: 0.6890 (t0) REVERT: B 222 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8430 (ttmt) REVERT: B 337 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.4885 (mtp-110) REVERT: B 339 ASP cc_start: 0.5765 (t0) cc_final: 0.5524 (t0) REVERT: B 361 TYR cc_start: 0.8111 (m-80) cc_final: 0.7757 (m-80) REVERT: C 210 ASP cc_start: 0.7451 (t70) cc_final: 0.6960 (t70) REVERT: C 222 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8491 (ttmt) REVERT: C 279 MET cc_start: 0.8608 (tpp) cc_final: 0.8352 (mmm) REVERT: C 337 ARG cc_start: 0.5946 (OUTLIER) cc_final: 0.4804 (mtp180) REVERT: D 96 ASP cc_start: 0.6375 (p0) cc_final: 0.5502 (p0) REVERT: D 212 ARG cc_start: 0.7414 (mmt-90) cc_final: 0.7121 (mmp80) REVERT: D 337 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.5431 (mtt180) REVERT: D 350 PHE cc_start: 0.7977 (t80) cc_final: 0.7620 (t80) outliers start: 20 outliers final: 0 residues processed: 377 average time/residue: 1.1823 time to fit residues: 489.3860 Evaluate side-chains 193 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 222 LYS Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain C residue 222 LYS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain D residue 337 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 81 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 131 ASN E 231 HIS A 131 ASN A 231 HIS ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN B 131 ASN B 166 GLN B 231 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN C 231 HIS C 282 GLN D 47 ASN D 131 ASN D 231 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14245 Z= 0.201 Angle : 0.690 15.115 19345 Z= 0.355 Chirality : 0.048 0.314 2205 Planarity : 0.006 0.052 2410 Dihedral : 6.522 56.562 2103 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.31 % Allowed : 11.19 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % 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: -1.41 (0.19), residues: 1705 helix: -0.19 (0.20), residues: 550 sheet: -0.73 (0.26), residues: 385 loop : -1.53 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 358 HIS 0.003 0.001 HIS C 231 PHE 0.021 0.002 PHE E 356 TYR 0.033 0.002 TYR D 317 ARG 0.012 0.001 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 ASP cc_start: 0.8097 (m-30) cc_final: 0.7856 (m-30) REVERT: E 159 LYS cc_start: 0.8511 (tmmt) cc_final: 0.8186 (mttt) REVERT: E 214 CYS cc_start: 0.5302 (p) cc_final: 0.5003 (p) REVERT: E 253 LEU cc_start: 0.8436 (mt) cc_final: 0.8173 (mt) REVERT: E 329 LYS cc_start: 0.5222 (OUTLIER) cc_final: 0.4948 (pptt) REVERT: E 337 ARG cc_start: 0.6865 (tpp80) cc_final: 0.5396 (mtt180) REVERT: E 363 LEU cc_start: 0.7743 (tp) cc_final: 0.7374 (tt) REVERT: A 96 ASP cc_start: 0.6096 (p0) cc_final: 0.5536 (p0) REVERT: A 105 MET cc_start: 0.7984 (mmm) cc_final: 0.7757 (mmm) REVERT: A 159 LYS cc_start: 0.8503 (tmmt) cc_final: 0.8048 (mttt) REVERT: A 227 GLU cc_start: 0.8326 (pt0) cc_final: 0.8090 (pt0) REVERT: A 243 MET cc_start: 0.8177 (mtm) cc_final: 0.7877 (mtt) REVERT: B 96 ASP cc_start: 0.5882 (p0) cc_final: 0.5212 (p0) REVERT: B 123 ASN cc_start: 0.8799 (p0) cc_final: 0.8593 (p0) REVERT: B 188 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: B 242 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7742 (mm-40) REVERT: B 243 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7323 (mtt) REVERT: C 159 LYS cc_start: 0.8545 (tmmt) cc_final: 0.8269 (mttm) REVERT: C 179 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8377 (mtt) REVERT: C 210 ASP cc_start: 0.7290 (t70) cc_final: 0.6755 (t70) REVERT: C 279 MET cc_start: 0.8660 (tpp) cc_final: 0.8401 (mmm) REVERT: C 287 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7254 (tpp80) REVERT: D 96 ASP cc_start: 0.6361 (p0) cc_final: 0.5598 (p0) REVERT: D 159 LYS cc_start: 0.8409 (tmmt) cc_final: 0.8111 (mttm) REVERT: D 173 GLU cc_start: 0.7858 (tt0) cc_final: 0.7470 (tt0) REVERT: D 193 GLN cc_start: 0.8522 (mt0) cc_final: 0.8212 (mt0) REVERT: D 242 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7389 (tm-30) REVERT: D 314 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7638 (tt) REVERT: D 329 LYS cc_start: 0.5693 (OUTLIER) cc_final: 0.5357 (pptt) outliers start: 50 outliers final: 18 residues processed: 260 average time/residue: 1.1156 time to fit residues: 320.8448 Evaluate side-chains 203 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN D 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14245 Z= 0.258 Angle : 0.739 17.627 19345 Z= 0.373 Chirality : 0.047 0.309 2205 Planarity : 0.005 0.049 2410 Dihedral : 6.076 50.188 2075 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.11 % Allowed : 13.11 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.64 (0.20), residues: 1705 helix: 0.84 (0.22), residues: 550 sheet: -0.54 (0.27), residues: 385 loop : -1.25 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 358 HIS 0.003 0.001 HIS E 125 PHE 0.024 0.002 PHE E 356 TYR 0.018 0.002 TYR E 317 ARG 0.007 0.001 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 187 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 107 ASP cc_start: 0.8088 (m-30) cc_final: 0.7854 (m-30) REVERT: E 210 ASP cc_start: 0.7350 (t70) cc_final: 0.6818 (t70) REVERT: E 214 CYS cc_start: 0.5427 (p) cc_final: 0.5140 (p) REVERT: E 242 GLN cc_start: 0.7571 (tp-100) cc_final: 0.7200 (tm-30) REVERT: E 253 LEU cc_start: 0.8516 (mt) cc_final: 0.8199 (mt) REVERT: E 337 ARG cc_start: 0.6659 (tpp80) cc_final: 0.5283 (mtt180) REVERT: E 363 LEU cc_start: 0.7749 (tp) cc_final: 0.7360 (tt) REVERT: A 105 MET cc_start: 0.8026 (mmm) cc_final: 0.7755 (mmm) REVERT: A 159 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8035 (mmtt) REVERT: A 193 GLN cc_start: 0.8484 (mt0) cc_final: 0.8107 (mt0) REVERT: A 243 MET cc_start: 0.8216 (mtm) cc_final: 0.7885 (mtt) REVERT: A 287 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7635 (tpp80) REVERT: B 96 ASP cc_start: 0.5903 (p0) cc_final: 0.5245 (p0) REVERT: B 179 MET cc_start: 0.8853 (mtp) cc_final: 0.8575 (mmt) REVERT: B 242 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7028 (tm-30) REVERT: B 243 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7218 (mtt) REVERT: C 159 LYS cc_start: 0.8557 (tmmt) cc_final: 0.8252 (mttm) REVERT: C 179 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8302 (mtt) REVERT: C 210 ASP cc_start: 0.7328 (t70) cc_final: 0.6816 (t70) REVERT: C 279 MET cc_start: 0.8692 (tpp) cc_final: 0.8478 (mmm) REVERT: C 287 ARG cc_start: 0.7678 (ttm110) cc_final: 0.7316 (ttp80) REVERT: D 96 ASP cc_start: 0.6546 (p0) cc_final: 0.6224 (p0) REVERT: D 159 LYS cc_start: 0.8446 (tmmt) cc_final: 0.8119 (mttm) REVERT: D 173 GLU cc_start: 0.7670 (tt0) cc_final: 0.7181 (tt0) REVERT: D 185 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: D 193 GLN cc_start: 0.8524 (mt0) cc_final: 0.8200 (mt0) REVERT: D 243 MET cc_start: 0.8099 (mtt) cc_final: 0.7888 (mtt) REVERT: D 277 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8201 (tt) outliers start: 47 outliers final: 25 residues processed: 222 average time/residue: 1.1087 time to fit residues: 273.0773 Evaluate side-chains 195 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 103 optimal weight: 0.0020 chunk 155 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 147 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN E 282 GLN A 82 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN B 82 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 282 GLN D 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14245 Z= 0.182 Angle : 0.649 13.969 19345 Z= 0.329 Chirality : 0.045 0.253 2205 Planarity : 0.004 0.045 2410 Dihedral : 5.754 52.654 2075 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.98 % Allowed : 14.17 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.19 (0.21), residues: 1705 helix: 1.54 (0.23), residues: 540 sheet: -0.41 (0.26), residues: 385 loop : -1.17 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 358 HIS 0.002 0.001 HIS B 231 PHE 0.022 0.001 PHE C 356 TYR 0.026 0.001 TYR C 317 ARG 0.005 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: E 107 ASP cc_start: 0.8062 (m-30) cc_final: 0.7833 (m-30) REVERT: E 210 ASP cc_start: 0.7368 (t70) cc_final: 0.6822 (t70) REVERT: E 214 CYS cc_start: 0.5353 (p) cc_final: 0.5073 (p) REVERT: E 242 GLN cc_start: 0.7610 (tp-100) cc_final: 0.7309 (tm-30) REVERT: E 253 LEU cc_start: 0.8519 (mt) cc_final: 0.8234 (mt) REVERT: E 337 ARG cc_start: 0.6590 (tpp80) cc_final: 0.5350 (mtt180) REVERT: E 363 LEU cc_start: 0.7633 (tp) cc_final: 0.7276 (tt) REVERT: A 105 MET cc_start: 0.7983 (mmm) cc_final: 0.7737 (mmm) REVERT: A 159 LYS cc_start: 0.8519 (tmmt) cc_final: 0.8000 (mmtt) REVERT: A 166 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7052 (mp10) REVERT: A 193 GLN cc_start: 0.8469 (mt0) cc_final: 0.8070 (mt0) REVERT: B 96 ASP cc_start: 0.5671 (p0) cc_final: 0.5146 (p0) REVERT: B 188 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 193 GLN cc_start: 0.8561 (mt0) cc_final: 0.8230 (mt0) REVERT: B 242 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7150 (tm-30) REVERT: B 243 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7037 (mtt) REVERT: C 157 ASP cc_start: 0.7705 (t70) cc_final: 0.7476 (t70) REVERT: C 159 LYS cc_start: 0.8558 (tmmt) cc_final: 0.8211 (mttt) REVERT: C 210 ASP cc_start: 0.7404 (t70) cc_final: 0.6878 (t70) REVERT: C 337 ARG cc_start: 0.6207 (mmm160) cc_final: 0.5040 (mtp180) REVERT: C 363 LEU cc_start: 0.7426 (tp) cc_final: 0.7069 (mp) REVERT: D 96 ASP cc_start: 0.6324 (p0) cc_final: 0.5959 (p0) REVERT: D 159 LYS cc_start: 0.8461 (tmmt) cc_final: 0.8174 (mttm) REVERT: D 173 GLU cc_start: 0.7661 (tt0) cc_final: 0.7223 (tt0) REVERT: D 193 GLN cc_start: 0.8523 (mt0) cc_final: 0.8205 (mt0) REVERT: D 243 MET cc_start: 0.8004 (mtt) cc_final: 0.7783 (mtt) REVERT: D 277 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8207 (tt) REVERT: D 314 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7263 (tt) REVERT: D 329 LYS cc_start: 0.5306 (OUTLIER) cc_final: 0.5022 (pptt) outliers start: 45 outliers final: 18 residues processed: 231 average time/residue: 1.1207 time to fit residues: 286.1503 Evaluate side-chains 190 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 122 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 282 GLN A 82 GLN B 82 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 242 GLN D 82 GLN D 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14245 Z= 0.233 Angle : 0.657 13.699 19345 Z= 0.333 Chirality : 0.045 0.242 2205 Planarity : 0.004 0.041 2410 Dihedral : 5.780 51.620 2075 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.25 % Allowed : 14.77 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.00 (0.21), residues: 1705 helix: 1.80 (0.23), residues: 545 sheet: -0.44 (0.26), residues: 385 loop : -1.06 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 358 HIS 0.003 0.001 HIS E 125 PHE 0.023 0.002 PHE C 356 TYR 0.020 0.002 TYR E 317 ARG 0.008 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.8021 (p0) cc_final: 0.7525 (m-30) REVERT: E 107 ASP cc_start: 0.8061 (m-30) cc_final: 0.7827 (m-30) REVERT: E 210 ASP cc_start: 0.7360 (t70) cc_final: 0.6789 (t70) REVERT: E 214 CYS cc_start: 0.5417 (p) cc_final: 0.5209 (p) REVERT: E 242 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7307 (tm-30) REVERT: E 253 LEU cc_start: 0.8555 (mt) cc_final: 0.8243 (mt) REVERT: E 337 ARG cc_start: 0.6340 (tpp80) cc_final: 0.5280 (mtt180) REVERT: A 105 MET cc_start: 0.8017 (mmm) cc_final: 0.7728 (mmm) REVERT: A 159 LYS cc_start: 0.8514 (tmmt) cc_final: 0.8145 (mmtt) REVERT: A 166 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7055 (mp10) REVERT: A 193 GLN cc_start: 0.8511 (mt0) cc_final: 0.8104 (mt0) REVERT: B 96 ASP cc_start: 0.5864 (p0) cc_final: 0.5150 (p0) REVERT: B 188 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: B 193 GLN cc_start: 0.8582 (mt0) cc_final: 0.8253 (mt0) REVERT: B 242 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7130 (tm-30) REVERT: B 243 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7059 (mtt) REVERT: C 159 LYS cc_start: 0.8587 (tmmt) cc_final: 0.8270 (mttm) REVERT: C 185 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: C 210 ASP cc_start: 0.7485 (t70) cc_final: 0.6966 (t70) REVERT: C 363 LEU cc_start: 0.7427 (tp) cc_final: 0.7088 (mp) REVERT: D 96 ASP cc_start: 0.6474 (p0) cc_final: 0.6151 (p0) REVERT: D 159 LYS cc_start: 0.8481 (tmmt) cc_final: 0.8162 (mttm) REVERT: D 173 GLU cc_start: 0.7685 (tt0) cc_final: 0.7238 (tt0) REVERT: D 185 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: D 193 GLN cc_start: 0.8525 (mt0) cc_final: 0.8214 (mt0) REVERT: D 314 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7232 (tt) REVERT: D 323 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6372 (mp) outliers start: 49 outliers final: 27 residues processed: 223 average time/residue: 1.0679 time to fit residues: 265.0467 Evaluate side-chains 204 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 86 optimal weight: 0.0870 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN A 82 GLN B 82 GLN C 82 GLN D 82 GLN D 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14245 Z= 0.166 Angle : 0.608 12.427 19345 Z= 0.308 Chirality : 0.044 0.249 2205 Planarity : 0.004 0.042 2410 Dihedral : 5.537 51.127 2075 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.19 % Allowed : 16.56 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.18 (0.21), residues: 1705 helix: 2.06 (0.23), residues: 560 sheet: -0.40 (0.27), residues: 385 loop : -1.08 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 358 HIS 0.002 0.001 HIS B 125 PHE 0.025 0.001 PHE C 356 TYR 0.020 0.001 TYR E 317 ARG 0.007 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.7896 (p0) cc_final: 0.7491 (m-30) REVERT: E 129 THR cc_start: 0.7936 (m) cc_final: 0.7505 (p) REVERT: E 210 ASP cc_start: 0.7366 (t70) cc_final: 0.6757 (t70) REVERT: E 214 CYS cc_start: 0.5389 (p) cc_final: 0.5167 (p) REVERT: E 253 LEU cc_start: 0.8541 (mt) cc_final: 0.8160 (mt) REVERT: E 314 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7843 (tt) REVERT: E 337 ARG cc_start: 0.6393 (tpp80) cc_final: 0.5316 (mtt180) REVERT: A 105 MET cc_start: 0.8023 (mmm) cc_final: 0.7747 (mmm) REVERT: A 159 LYS cc_start: 0.8534 (tmmt) cc_final: 0.8077 (mttt) REVERT: A 166 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: A 193 GLN cc_start: 0.8491 (mt0) cc_final: 0.8167 (mt0) REVERT: A 361 TYR cc_start: 0.8256 (m-80) cc_final: 0.7629 (m-80) REVERT: B 96 ASP cc_start: 0.5844 (p0) cc_final: 0.5247 (p0) REVERT: B 188 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: B 193 GLN cc_start: 0.8591 (mt0) cc_final: 0.8311 (mt0) REVERT: B 242 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7253 (tm-30) REVERT: B 243 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.6951 (mtt) REVERT: C 159 LYS cc_start: 0.8518 (tmmt) cc_final: 0.8262 (mttm) REVERT: C 210 ASP cc_start: 0.7424 (t70) cc_final: 0.6864 (t70) REVERT: C 242 GLN cc_start: 0.7553 (tp-100) cc_final: 0.7137 (tm-30) REVERT: C 300 ASP cc_start: 0.8079 (m-30) cc_final: 0.7768 (m-30) REVERT: C 337 ARG cc_start: 0.6407 (mmm160) cc_final: 0.5076 (mtp180) REVERT: C 363 LEU cc_start: 0.7369 (tp) cc_final: 0.7131 (mp) REVERT: D 96 ASP cc_start: 0.6371 (p0) cc_final: 0.5937 (p0) REVERT: D 159 LYS cc_start: 0.8469 (tmmt) cc_final: 0.8157 (mttm) REVERT: D 173 GLU cc_start: 0.7568 (tt0) cc_final: 0.7356 (tt0) REVERT: D 185 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: D 193 GLN cc_start: 0.8514 (mt0) cc_final: 0.8201 (mt0) REVERT: D 323 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6344 (mp) outliers start: 33 outliers final: 21 residues processed: 220 average time/residue: 1.0633 time to fit residues: 260.6112 Evaluate side-chains 200 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 323 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 91 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN A 82 GLN B 82 GLN D 77 ASN D 82 GLN D 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14245 Z= 0.186 Angle : 0.610 12.782 19345 Z= 0.310 Chirality : 0.044 0.248 2205 Planarity : 0.004 0.041 2410 Dihedral : 5.507 50.535 2075 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.45 % Allowed : 16.09 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.25 (0.21), residues: 1705 helix: 2.16 (0.23), residues: 560 sheet: -0.38 (0.27), residues: 385 loop : -1.08 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.002 0.001 HIS E 125 PHE 0.025 0.001 PHE C 356 TYR 0.017 0.001 TYR E 317 ARG 0.006 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.7877 (p0) cc_final: 0.7521 (m-30) REVERT: E 156 MET cc_start: 0.8909 (mtt) cc_final: 0.8706 (mtm) REVERT: E 214 CYS cc_start: 0.5429 (p) cc_final: 0.5196 (p) REVERT: E 253 LEU cc_start: 0.8547 (mt) cc_final: 0.8145 (mt) REVERT: E 337 ARG cc_start: 0.6354 (tpp80) cc_final: 0.5336 (mtt180) REVERT: E 363 LEU cc_start: 0.7175 (tp) cc_final: 0.6841 (mp) REVERT: A 105 MET cc_start: 0.8038 (mmm) cc_final: 0.7752 (mmm) REVERT: A 159 LYS cc_start: 0.8530 (tmmt) cc_final: 0.8100 (mmtt) REVERT: A 193 GLN cc_start: 0.8500 (mt0) cc_final: 0.8171 (mt0) REVERT: B 96 ASP cc_start: 0.5911 (p0) cc_final: 0.5340 (p0) REVERT: B 188 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: B 193 GLN cc_start: 0.8589 (mt0) cc_final: 0.8247 (mt0) REVERT: B 242 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7206 (tm-30) REVERT: B 243 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.6947 (mtt) REVERT: C 159 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8281 (mttm) REVERT: C 185 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: C 210 ASP cc_start: 0.7419 (t70) cc_final: 0.6885 (t70) REVERT: C 242 GLN cc_start: 0.7576 (tp-100) cc_final: 0.7048 (tm-30) REVERT: C 300 ASP cc_start: 0.8060 (m-30) cc_final: 0.7767 (m-30) REVERT: C 337 ARG cc_start: 0.6425 (mmm160) cc_final: 0.5123 (mtp-110) REVERT: C 363 LEU cc_start: 0.7395 (tp) cc_final: 0.7181 (mp) REVERT: D 96 ASP cc_start: 0.6416 (p0) cc_final: 0.5965 (p0) REVERT: D 159 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8166 (mttm) REVERT: D 173 GLU cc_start: 0.7648 (tt0) cc_final: 0.7412 (tt0) REVERT: D 185 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: D 193 GLN cc_start: 0.8516 (mt0) cc_final: 0.8199 (mt0) REVERT: D 323 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6332 (mp) outliers start: 37 outliers final: 27 residues processed: 206 average time/residue: 1.1055 time to fit residues: 252.5787 Evaluate side-chains 206 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14245 Z= 0.233 Angle : 0.631 13.160 19345 Z= 0.320 Chirality : 0.045 0.242 2205 Planarity : 0.004 0.039 2410 Dihedral : 5.561 49.743 2075 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.58 % Allowed : 16.29 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.27 (0.21), residues: 1705 helix: 2.20 (0.23), residues: 560 sheet: -0.40 (0.27), residues: 385 loop : -1.06 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 358 HIS 0.003 0.001 HIS E 125 PHE 0.027 0.002 PHE C 356 TYR 0.015 0.002 TYR C 144 ARG 0.006 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 1.502 Fit side-chains REVERT: E 100 ASP cc_start: 0.7868 (p0) cc_final: 0.7531 (m-30) REVERT: E 214 CYS cc_start: 0.5448 (p) cc_final: 0.5221 (p) REVERT: E 253 LEU cc_start: 0.8566 (mt) cc_final: 0.8149 (mt) REVERT: E 337 ARG cc_start: 0.6460 (tpp80) cc_final: 0.5448 (mtt180) REVERT: E 339 ASP cc_start: 0.6331 (t0) cc_final: 0.6081 (t0) REVERT: E 363 LEU cc_start: 0.7347 (tp) cc_final: 0.7082 (mp) REVERT: A 105 MET cc_start: 0.8055 (mmm) cc_final: 0.7766 (mmm) REVERT: A 159 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8118 (mmtt) REVERT: A 166 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.6928 (mp10) REVERT: A 193 GLN cc_start: 0.8520 (mt0) cc_final: 0.8138 (mt0) REVERT: B 96 ASP cc_start: 0.5953 (p0) cc_final: 0.5325 (p0) REVERT: B 188 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: B 193 GLN cc_start: 0.8578 (mt0) cc_final: 0.8214 (mt0) REVERT: B 242 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7109 (tm-30) REVERT: B 243 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7026 (mtt) REVERT: C 159 LYS cc_start: 0.8584 (tmmt) cc_final: 0.8259 (mptp) REVERT: C 185 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: C 210 ASP cc_start: 0.7422 (t70) cc_final: 0.6913 (t70) REVERT: C 242 GLN cc_start: 0.7640 (tp-100) cc_final: 0.7038 (tm-30) REVERT: C 300 ASP cc_start: 0.8034 (m-30) cc_final: 0.7797 (m-30) REVERT: C 337 ARG cc_start: 0.6518 (mmm160) cc_final: 0.5220 (mtp180) REVERT: C 363 LEU cc_start: 0.7375 (tp) cc_final: 0.7134 (mp) REVERT: D 96 ASP cc_start: 0.6520 (p0) cc_final: 0.6244 (p0) REVERT: D 159 LYS cc_start: 0.8503 (tmmt) cc_final: 0.8147 (mttm) REVERT: D 173 GLU cc_start: 0.7691 (tt0) cc_final: 0.7458 (tt0) REVERT: D 185 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: D 193 GLN cc_start: 0.8524 (mt0) cc_final: 0.8202 (mt0) REVERT: D 323 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6544 (mp) outliers start: 39 outliers final: 28 residues processed: 206 average time/residue: 1.1015 time to fit residues: 251.4432 Evaluate side-chains 209 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14245 Z= 0.211 Angle : 0.619 12.913 19345 Z= 0.314 Chirality : 0.044 0.244 2205 Planarity : 0.004 0.037 2410 Dihedral : 5.513 50.279 2075 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.58 % Allowed : 16.69 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.30 (0.21), residues: 1705 helix: 2.25 (0.23), residues: 560 sheet: -0.40 (0.27), residues: 385 loop : -1.06 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 358 HIS 0.002 0.001 HIS E 125 PHE 0.027 0.001 PHE E 356 TYR 0.014 0.001 TYR C 144 ARG 0.007 0.001 ARG C 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: E 100 ASP cc_start: 0.7818 (p0) cc_final: 0.7549 (m-30) REVERT: E 214 CYS cc_start: 0.5455 (p) cc_final: 0.5231 (p) REVERT: E 243 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7463 (ptp) REVERT: E 253 LEU cc_start: 0.8569 (mt) cc_final: 0.8154 (mt) REVERT: E 337 ARG cc_start: 0.6414 (tpp80) cc_final: 0.5470 (mtp180) REVERT: E 363 LEU cc_start: 0.7429 (tp) cc_final: 0.7207 (mp) REVERT: A 105 MET cc_start: 0.8046 (mmm) cc_final: 0.7760 (mmm) REVERT: A 159 LYS cc_start: 0.8551 (tmmt) cc_final: 0.8118 (mmtt) REVERT: A 166 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.6839 (mp10) REVERT: A 193 GLN cc_start: 0.8507 (mt0) cc_final: 0.8171 (mt0) REVERT: B 96 ASP cc_start: 0.5956 (p0) cc_final: 0.5329 (p0) REVERT: B 188 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: B 193 GLN cc_start: 0.8583 (mt0) cc_final: 0.8231 (mt0) REVERT: B 242 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7058 (tm-30) REVERT: B 243 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7020 (mtt) REVERT: C 159 LYS cc_start: 0.8562 (tmmt) cc_final: 0.8280 (mttm) REVERT: C 185 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: C 189 LYS cc_start: 0.8375 (tptp) cc_final: 0.8118 (tppp) REVERT: C 210 ASP cc_start: 0.7420 (t70) cc_final: 0.6949 (t70) REVERT: C 242 GLN cc_start: 0.7580 (tp-100) cc_final: 0.6987 (tm-30) REVERT: C 300 ASP cc_start: 0.8021 (m-30) cc_final: 0.7786 (m-30) REVERT: C 337 ARG cc_start: 0.6473 (mmm160) cc_final: 0.5148 (mtp180) REVERT: C 363 LEU cc_start: 0.7383 (tp) cc_final: 0.7142 (mp) REVERT: D 96 ASP cc_start: 0.6501 (p0) cc_final: 0.6256 (p0) REVERT: D 159 LYS cc_start: 0.8474 (tmmt) cc_final: 0.8140 (mttm) REVERT: D 173 GLU cc_start: 0.7685 (tt0) cc_final: 0.7448 (tt0) REVERT: D 185 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: D 193 GLN cc_start: 0.8521 (mt0) cc_final: 0.8197 (mt0) REVERT: D 323 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6546 (mp) outliers start: 39 outliers final: 29 residues processed: 210 average time/residue: 1.1459 time to fit residues: 268.2051 Evaluate side-chains 209 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 323 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 169 optimal weight: 0.1980 chunk 155 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 143 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN D 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14245 Z= 0.171 Angle : 0.592 12.471 19345 Z= 0.303 Chirality : 0.044 0.248 2205 Planarity : 0.004 0.038 2410 Dihedral : 5.365 50.211 2075 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.45 % Allowed : 17.02 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.32 (0.21), residues: 1705 helix: 2.47 (0.23), residues: 550 sheet: -0.41 (0.26), residues: 385 loop : -1.16 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 358 HIS 0.003 0.001 HIS B 217 PHE 0.029 0.001 PHE E 356 TYR 0.011 0.001 TYR E 144 ARG 0.006 0.000 ARG E 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 183 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: E 214 CYS cc_start: 0.5448 (p) cc_final: 0.5216 (p) REVERT: E 253 LEU cc_start: 0.8545 (mt) cc_final: 0.8148 (mt) REVERT: E 337 ARG cc_start: 0.6422 (tpp80) cc_final: 0.5498 (mtt180) REVERT: A 105 MET cc_start: 0.8004 (mmm) cc_final: 0.7746 (mmm) REVERT: A 159 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8106 (mmtt) REVERT: A 166 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: A 193 GLN cc_start: 0.8490 (mt0) cc_final: 0.8153 (mt0) REVERT: B 96 ASP cc_start: 0.5935 (p0) cc_final: 0.5363 (p0) REVERT: B 188 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: B 193 GLN cc_start: 0.8588 (mt0) cc_final: 0.8229 (mt0) REVERT: B 242 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7124 (tm-30) REVERT: B 243 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6968 (mtt) REVERT: C 159 LYS cc_start: 0.8576 (tmmt) cc_final: 0.8233 (mttt) REVERT: C 185 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6901 (mm-30) REVERT: C 189 LYS cc_start: 0.8320 (tptp) cc_final: 0.8063 (tppp) REVERT: C 210 ASP cc_start: 0.7399 (t70) cc_final: 0.6958 (t70) REVERT: C 242 GLN cc_start: 0.7533 (tp-100) cc_final: 0.6986 (tm-30) REVERT: C 300 ASP cc_start: 0.8011 (m-30) cc_final: 0.7779 (m-30) REVERT: C 337 ARG cc_start: 0.6574 (mmm160) cc_final: 0.5191 (mtp180) REVERT: C 363 LEU cc_start: 0.7391 (tp) cc_final: 0.7176 (mp) REVERT: D 96 ASP cc_start: 0.6500 (p0) cc_final: 0.6258 (p0) REVERT: D 159 LYS cc_start: 0.8463 (tmmt) cc_final: 0.8133 (mttm) REVERT: D 173 GLU cc_start: 0.7651 (tt0) cc_final: 0.7380 (tt0) REVERT: D 185 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7068 (mt-10) REVERT: D 193 GLN cc_start: 0.8504 (mt0) cc_final: 0.8188 (mt0) outliers start: 37 outliers final: 26 residues processed: 210 average time/residue: 1.1631 time to fit residues: 269.6996 Evaluate side-chains 205 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0770 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN D 77 ASN D 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103225 restraints weight = 60992.565| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.91 r_work: 0.3010 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14245 Z= 0.187 Angle : 0.602 12.647 19345 Z= 0.306 Chirality : 0.044 0.248 2205 Planarity : 0.004 0.036 2410 Dihedral : 5.317 49.545 2075 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.32 % Allowed : 17.42 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.33 (0.21), residues: 1705 helix: 2.35 (0.23), residues: 560 sheet: -0.43 (0.26), residues: 385 loop : -1.08 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.002 0.001 HIS E 125 PHE 0.029 0.001 PHE E 356 TYR 0.012 0.001 TYR E 144 ARG 0.006 0.001 ARG E 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5196.87 seconds wall clock time: 92 minutes 50.94 seconds (5570.94 seconds total)