Starting phenix.real_space_refine on Wed Apr 10 06:04:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4s_41893/04_2024/8u4s_41893_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6024 atoms to isotropic. 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 P 3 5.49 5 S 69 5.16 5 C 8316 2.51 5 N 2064 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 86": "OE1" <-> "OE2" Residue "L ASP 87": "OD1" <-> "OD2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "R ASP 133": "OD1" <-> "OD2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "E GLU 86": "OE1" <-> "OE2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "G ASP 133": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12684 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 856 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2297 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain: "A" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 856 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "C" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2297 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain: "E" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 856 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "G" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2297 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain: "R" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'CLR': 2, 'D21': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'CLR': 2, 'D21': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'CLR': 2, 'D21': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 6.85, per 1000 atoms: 0.54 Number of scatterers: 12684 At special positions: 0 Unit cell: (105.4, 107.1, 107.1, 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) S 69 16.00 P 3 15.00 O 2232 8.00 N 2064 7.00 C 8316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 274 " distance=2.03 Simple disulfide: pdb=" SG CYS G 109 " - pdb=" SG CYS G 186 " distance=2.03 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 Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.1 seconds 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 15 sheets defined 43.2% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'R' and resid 34 through 63 removed outlier: 3.761A pdb=" N ILE R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 72 through 99 removed outlier: 3.665A pdb=" N TYR R 76 " --> pdb=" O MET R 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU R 91 " --> pdb=" O PHE R 87 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 105 through 138 removed outlier: 3.810A pdb=" N LEU R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR R 121 " --> pdb=" O THR R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 155 through 174 removed outlier: 4.748A pdb=" N ILE R 162 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Proline residue: R 163 - end of helix removed outlier: 3.722A pdb=" N THR R 168 " --> pdb=" O ALA R 164 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 193 through 228 Proline residue: R 211 - end of helix removed outlier: 3.800A pdb=" N CYS R 220 " --> pdb=" O LEU R 216 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER R 227 " --> pdb=" O ILE R 223 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 266 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 275 through 301 removed outlier: 3.987A pdb=" N PHE R 292 " --> pdb=" O GLU R 288 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE R 293 " --> pdb=" O ALA R 289 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N HIS R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N CYS R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'C' and resid 34 through 63 removed outlier: 3.762A pdb=" N ILE C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 72 through 99 removed outlier: 3.666A pdb=" N TYR C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Proline residue: C 92 - end of helix Processing helix chain 'C' and resid 105 through 138 removed outlier: 3.811A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 155 through 174 removed outlier: 4.749A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix removed outlier: 3.722A pdb=" N THR C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 193 through 228 Proline residue: C 211 - end of helix removed outlier: 3.801A pdb=" N CYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N HIS C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 266 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 275 through 301 removed outlier: 3.987A pdb=" N PHE C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N HIS C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N CYS C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS C 296 " --> pdb=" O PHE C 292 " (cutoff:3.500A) Proline residue: C 299 - end of helix Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'G' and resid 34 through 63 removed outlier: 3.762A pdb=" N ILE G 39 " --> pdb=" O ASN G 35 " (cutoff:3.500A) Proline residue: G 42 - end of helix Processing helix chain 'G' and resid 72 through 99 removed outlier: 3.666A pdb=" N TYR G 76 " --> pdb=" O MET G 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) Proline residue: G 92 - end of helix Processing helix chain 'G' and resid 105 through 138 removed outlier: 3.810A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 153 Processing helix chain 'G' and resid 155 through 174 removed outlier: 4.748A pdb=" N ILE G 162 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Proline residue: G 163 - end of helix removed outlier: 3.722A pdb=" N THR G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'G' and resid 193 through 228 Proline residue: G 211 - end of helix removed outlier: 3.801A pdb=" N CYS G 220 " --> pdb=" O LEU G 216 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N HIS G 228 " --> pdb=" O SER G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 266 Proline residue: G 254 - end of helix Processing helix chain 'G' and resid 275 through 301 removed outlier: 3.986A pdb=" N PHE G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE G 293 " --> pdb=" O ALA G 289 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS G 294 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N CYS G 295 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS G 296 " --> pdb=" O PHE G 292 " (cutoff:3.500A) Proline residue: G 299 - end of helix Processing sheet with id= A, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.926A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 90 through 95 removed outlier: 3.575A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN L 42 " --> pdb=" O ARG L 51 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARG L 51 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= D, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.635A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA H 40 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'R' and resid 175 through 180 removed outlier: 3.525A pdb=" N ASN R 176 " --> pdb=" O ASP R 187 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP R 187 " --> pdb=" O ASN R 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 180 " --> pdb=" O ARG R 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.926A pdb=" N THR A 5 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 24 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 90 through 95 removed outlier: 3.574A pdb=" N ILE A 53 " --> pdb=" O TRP A 40 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN A 42 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ARG A 51 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= I, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.635A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA B 40 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 45 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 175 through 180 removed outlier: 3.525A pdb=" N ASN C 176 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 187 " --> pdb=" O ASN C 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 180 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.926A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 24 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 90 through 95 removed outlier: 3.574A pdb=" N ILE E 53 " --> pdb=" O TRP E 40 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN E 42 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 3 through 6 Processing sheet with id= N, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.635A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA F 40 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE F 45 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 175 through 180 removed outlier: 3.525A pdb=" N ASN G 176 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP G 187 " --> pdb=" O ASN G 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G 180 " --> pdb=" O ARG G 183 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1728 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: 3.52 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3695 1.34 - 1.47: 3563 1.47 - 1.59: 5663 1.59 - 1.72: 0 1.72 - 1.85: 102 Bond restraints: 13023 Sorted by residual: bond pdb=" O22 D21 R 702 " pdb=" P23 D21 R 702 " ideal model delta sigma weight residual 1.643 1.853 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" O22 D21 G 702 " pdb=" P23 D21 G 702 " ideal model delta sigma weight residual 1.643 1.853 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" O22 D21 C 702 " pdb=" P23 D21 C 702 " ideal model delta sigma weight residual 1.643 1.853 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C16 D21 G 702 " pdb=" O18 D21 G 702 " ideal model delta sigma weight residual 1.408 1.343 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C16 D21 R 702 " pdb=" O18 D21 R 702 " ideal model delta sigma weight residual 1.408 1.343 0.065 2.00e-02 2.50e+03 1.04e+01 ... (remaining 13018 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.89: 261 105.89 - 112.98: 7014 112.98 - 120.06: 4594 120.06 - 127.15: 5680 127.15 - 134.24: 160 Bond angle restraints: 17709 Sorted by residual: angle pdb=" CB MET F 113 " pdb=" CG MET F 113 " pdb=" SD MET F 113 " ideal model delta sigma weight residual 112.70 133.45 -20.75 3.00e+00 1.11e-01 4.78e+01 angle pdb=" CB MET H 113 " pdb=" CG MET H 113 " pdb=" SD MET H 113 " ideal model delta sigma weight residual 112.70 133.43 -20.73 3.00e+00 1.11e-01 4.77e+01 angle pdb=" CB MET B 113 " pdb=" CG MET B 113 " pdb=" SD MET B 113 " ideal model delta sigma weight residual 112.70 133.40 -20.70 3.00e+00 1.11e-01 4.76e+01 angle pdb=" CA MET B 113 " pdb=" CB MET B 113 " pdb=" CG MET B 113 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" CA MET H 113 " pdb=" CB MET H 113 " pdb=" CG MET H 113 " ideal model delta sigma weight residual 114.10 123.15 -9.05 2.00e+00 2.50e-01 2.05e+01 ... (remaining 17704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 7040 17.20 - 34.40: 613 34.40 - 51.60: 176 51.60 - 68.80: 55 68.80 - 86.00: 18 Dihedral angle restraints: 7902 sinusoidal: 3372 harmonic: 4530 Sorted by residual: dihedral pdb=" CB CYS C 28 " pdb=" SG CYS C 28 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual 93.00 168.19 -75.19 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual 93.00 168.17 -75.17 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS G 28 " pdb=" SG CYS G 28 " pdb=" SG CYS G 274 " pdb=" CB CYS G 274 " ideal model delta sinusoidal sigma weight residual 93.00 168.14 -75.14 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 7899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1759 0.077 - 0.155: 203 0.155 - 0.232: 3 0.232 - 0.309: 20 0.309 - 0.386: 7 Chirality restraints: 1992 Sorted by residual: chirality pdb=" C17 CLR G 701 " pdb=" C13 CLR G 701 " pdb=" C16 CLR G 701 " pdb=" C20 CLR G 701 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C17 CLR C 701 " pdb=" C13 CLR C 701 " pdb=" C16 CLR C 701 " pdb=" C20 CLR C 701 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C17 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C16 CLR R 701 " pdb=" C20 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1989 not shown) Planarity restraints: 2151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 44 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO L 45 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 44 " -0.055 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO E 45 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 45 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 44 " -0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO A 45 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.046 5.00e-02 4.00e+02 ... (remaining 2148 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 952 2.74 - 3.28: 12405 3.28 - 3.82: 20149 3.82 - 4.36: 23013 4.36 - 4.90: 41823 Nonbonded interactions: 98342 Sorted by model distance: nonbonded pdb=" OH TYR A 54 " pdb=" OD2 ASP C 182 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR L 54 " pdb=" OD2 ASP R 182 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR E 54 " pdb=" OD2 ASP G 182 " model vdw 2.202 2.440 nonbonded pdb=" OG SER L 25 " pdb=" O GLN L 27 " model vdw 2.235 2.440 nonbonded pdb=" OG SER A 25 " pdb=" O GLN A 27 " model vdw 2.236 2.440 ... (remaining 98337 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 10.380 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 34.720 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.006 0.210 13023 Z= 0.373 Angle : 0.915 20.751 17709 Z= 0.408 Chirality : 0.057 0.386 1992 Planarity : 0.006 0.083 2151 Dihedral : 14.896 86.000 4974 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.67 % Allowed : 1.11 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.41 (0.22), residues: 1539 helix: 1.92 (0.21), residues: 651 sheet: 0.13 (0.27), residues: 348 loop : -1.74 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 195 HIS 0.002 0.001 HIS G 281 PHE 0.021 0.001 PHE A 90 TYR 0.014 0.001 TYR A 31 ARG 0.009 0.001 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 297 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: H 58 ARG cc_start: 0.7843 (pmt-80) cc_final: 0.7348 (pmt-80) REVERT: R 153 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: R 195 TRP cc_start: 0.7196 (m100) cc_final: 0.5974 (m-90) REVERT: R 205 MET cc_start: 0.7469 (tmm) cc_final: 0.7249 (tmm) REVERT: R 284 ILE cc_start: 0.8201 (mt) cc_final: 0.7877 (mt) REVERT: C 153 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: C 195 TRP cc_start: 0.7146 (m100) cc_final: 0.5994 (m-90) REVERT: F 58 ARG cc_start: 0.7767 (pmt-80) cc_final: 0.7243 (pmt-80) REVERT: G 153 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: G 195 TRP cc_start: 0.7263 (m100) cc_final: 0.5967 (m-90) outliers start: 9 outliers final: 6 residues processed: 297 average time/residue: 0.2751 time to fit residues: 114.1259 Evaluate side-chains 260 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain R residue 153 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain G residue 153 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13023 Z= 0.246 Angle : 0.580 6.369 17709 Z= 0.302 Chirality : 0.044 0.149 1992 Planarity : 0.005 0.047 2151 Dihedral : 8.969 56.972 2214 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.44 % Allowed : 10.94 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.50 (0.22), residues: 1539 helix: 2.13 (0.21), residues: 639 sheet: 0.04 (0.27), residues: 363 loop : -1.75 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.004 0.001 HIS C 203 PHE 0.014 0.001 PHE G 29 TYR 0.011 0.001 TYR F 111 ARG 0.005 0.001 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 268 time to evaluate : 1.367 Fit side-chains REVERT: L 60 ASP cc_start: 0.8515 (p0) cc_final: 0.8080 (p0) REVERT: H 58 ARG cc_start: 0.7848 (pmt-80) cc_final: 0.7499 (pmt-80) REVERT: H 106 ASN cc_start: 0.8029 (m110) cc_final: 0.7407 (m110) REVERT: R 195 TRP cc_start: 0.7351 (m100) cc_final: 0.6325 (m-90) REVERT: A 60 ASP cc_start: 0.8502 (p0) cc_final: 0.8248 (p0) REVERT: A 79 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8444 (ptpp) REVERT: B 57 ASN cc_start: 0.8427 (m110) cc_final: 0.8205 (m-40) REVERT: B 106 ASN cc_start: 0.8080 (m110) cc_final: 0.7824 (m-40) REVERT: C 195 TRP cc_start: 0.7451 (m100) cc_final: 0.6441 (m-90) REVERT: C 205 MET cc_start: 0.7764 (tmm) cc_final: 0.7331 (tmm) REVERT: F 58 ARG cc_start: 0.7851 (pmt-80) cc_final: 0.7367 (pmt-80) REVERT: F 81 MET cc_start: 0.7903 (tmm) cc_final: 0.7681 (ttt) REVERT: F 106 ASN cc_start: 0.8125 (m110) cc_final: 0.7731 (m-40) REVERT: G 195 TRP cc_start: 0.7300 (m100) cc_final: 0.6325 (m-90) REVERT: G 253 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8534 (tt) outliers start: 33 outliers final: 17 residues processed: 274 average time/residue: 0.2712 time to fit residues: 103.9507 Evaluate side-chains 267 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 248 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 0.0020 chunk 47 optimal weight: 0.0000 chunk 111 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13023 Z= 0.224 Angle : 0.556 6.424 17709 Z= 0.291 Chirality : 0.043 0.156 1992 Planarity : 0.004 0.039 2151 Dihedral : 7.764 58.384 2196 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.66 % Allowed : 14.19 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.54 (0.22), residues: 1539 helix: 2.06 (0.21), residues: 642 sheet: 0.25 (0.28), residues: 351 loop : -1.72 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 116 HIS 0.003 0.001 HIS C 203 PHE 0.013 0.001 PHE G 29 TYR 0.008 0.001 TYR G 302 ARG 0.005 0.001 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 60 ASP cc_start: 0.8562 (p0) cc_final: 0.8226 (p0) REVERT: H 106 ASN cc_start: 0.8130 (m110) cc_final: 0.7533 (m110) REVERT: R 253 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8489 (tt) REVERT: A 79 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8473 (ptpp) REVERT: B 57 ASN cc_start: 0.8558 (m110) cc_final: 0.8230 (m-40) REVERT: B 106 ASN cc_start: 0.8234 (m110) cc_final: 0.7950 (m-40) REVERT: C 195 TRP cc_start: 0.7587 (m100) cc_final: 0.6651 (m-90) REVERT: C 205 MET cc_start: 0.7728 (tmm) cc_final: 0.7298 (tmm) REVERT: F 106 ASN cc_start: 0.8143 (m110) cc_final: 0.7872 (m-40) REVERT: G 195 TRP cc_start: 0.7475 (m100) cc_final: 0.6582 (m-90) REVERT: G 253 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8505 (tt) outliers start: 36 outliers final: 26 residues processed: 289 average time/residue: 0.2567 time to fit residues: 105.3034 Evaluate side-chains 285 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain G residue 253 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 123 optimal weight: 0.0980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13023 Z= 0.226 Angle : 0.563 6.735 17709 Z= 0.291 Chirality : 0.043 0.168 1992 Planarity : 0.004 0.038 2151 Dihedral : 7.519 56.772 2193 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.62 % Allowed : 14.93 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.48 (0.22), residues: 1539 helix: 1.99 (0.21), residues: 642 sheet: 0.14 (0.28), residues: 360 loop : -1.66 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 50 HIS 0.003 0.001 HIS R 281 PHE 0.011 0.001 PHE G 29 TYR 0.009 0.001 TYR A 54 ARG 0.005 0.000 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 277 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 ARG cc_start: 0.8608 (ptt-90) cc_final: 0.8081 (ptt90) REVERT: L 60 ASP cc_start: 0.8584 (p0) cc_final: 0.8280 (p0) REVERT: H 106 ASN cc_start: 0.8276 (m110) cc_final: 0.7757 (m110) REVERT: R 65 TYR cc_start: 0.8433 (t80) cc_final: 0.8150 (t80) REVERT: A 79 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8462 (ptpp) REVERT: B 106 ASN cc_start: 0.8225 (m110) cc_final: 0.7968 (m-40) REVERT: C 272 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6295 (mp10) REVERT: G 138 ILE cc_start: 0.8895 (mt) cc_final: 0.8695 (mt) REVERT: G 195 TRP cc_start: 0.7517 (m100) cc_final: 0.6659 (m-90) REVERT: G 253 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8526 (tt) REVERT: G 272 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6457 (mp10) outliers start: 49 outliers final: 33 residues processed: 294 average time/residue: 0.2573 time to fit residues: 108.2346 Evaluate side-chains 301 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 264 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13023 Z= 0.284 Angle : 0.603 9.049 17709 Z= 0.312 Chirality : 0.045 0.184 1992 Planarity : 0.004 0.040 2151 Dihedral : 7.688 59.490 2193 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.66 % Allowed : 15.37 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.43 (0.22), residues: 1539 helix: 1.87 (0.21), residues: 642 sheet: 0.29 (0.28), residues: 351 loop : -1.71 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 47 HIS 0.005 0.001 HIS G 203 PHE 0.012 0.001 PHE C 29 TYR 0.009 0.001 TYR A 54 ARG 0.006 0.001 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 279 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 ARG cc_start: 0.8603 (ptt-90) cc_final: 0.8064 (ptt90) REVERT: L 94 MET cc_start: 0.8317 (ptm) cc_final: 0.8013 (ptm) REVERT: H 106 ASN cc_start: 0.8407 (m110) cc_final: 0.7924 (m110) REVERT: H 113 MET cc_start: 0.8248 (mmm) cc_final: 0.8042 (tpp) REVERT: R 65 TYR cc_start: 0.8475 (t80) cc_final: 0.8208 (t80) REVERT: R 80 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7691 (tt) REVERT: R 84 ASP cc_start: 0.8307 (m-30) cc_final: 0.8033 (m-30) REVERT: R 253 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8522 (tt) REVERT: R 272 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6329 (mp10) REVERT: A 79 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8467 (ptpp) REVERT: B 57 ASN cc_start: 0.8755 (m110) cc_final: 0.8437 (m110) REVERT: B 106 ASN cc_start: 0.8409 (m110) cc_final: 0.8183 (m-40) REVERT: C 132 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8394 (tt) REVERT: C 272 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.6412 (mp10) REVERT: G 205 MET cc_start: 0.7645 (tmm) cc_final: 0.7434 (tpp) REVERT: G 253 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8554 (tt) REVERT: G 272 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6604 (mp10) outliers start: 63 outliers final: 45 residues processed: 301 average time/residue: 0.2320 time to fit residues: 99.6755 Evaluate side-chains 322 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 269 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain R residue 274 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13023 Z= 0.187 Angle : 0.559 7.825 17709 Z= 0.287 Chirality : 0.043 0.187 1992 Planarity : 0.004 0.039 2151 Dihedral : 7.304 55.887 2193 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.99 % Allowed : 17.29 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.50 (0.22), residues: 1539 helix: 1.97 (0.21), residues: 642 sheet: 0.30 (0.28), residues: 351 loop : -1.72 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.004 0.001 HIS R 281 PHE 0.007 0.001 PHE G 29 TYR 0.010 0.001 TYR H 54 ARG 0.007 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 276 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 59 ARG cc_start: 0.8505 (ptt-90) cc_final: 0.8069 (ptt90) REVERT: L 94 MET cc_start: 0.8336 (ptm) cc_final: 0.8021 (ptm) REVERT: H 91 THR cc_start: 0.8407 (t) cc_final: 0.8206 (t) REVERT: H 106 ASN cc_start: 0.8345 (m110) cc_final: 0.7956 (m-40) REVERT: R 65 TYR cc_start: 0.8447 (t80) cc_final: 0.8169 (t80) REVERT: R 253 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8466 (tt) REVERT: R 272 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6300 (mp10) REVERT: A 79 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8460 (ptpp) REVERT: B 57 ASN cc_start: 0.8708 (m110) cc_final: 0.8326 (m110) REVERT: B 106 ASN cc_start: 0.8365 (m-40) cc_final: 0.8141 (m-40) REVERT: C 132 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8366 (tt) REVERT: G 195 TRP cc_start: 0.7516 (m100) cc_final: 0.6545 (m-90) REVERT: G 205 MET cc_start: 0.7613 (tmm) cc_final: 0.7388 (tpp) REVERT: G 253 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8523 (tt) outliers start: 54 outliers final: 44 residues processed: 301 average time/residue: 0.2550 time to fit residues: 109.7085 Evaluate side-chains 317 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 268 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain R residue 274 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13023 Z= 0.299 Angle : 0.621 8.453 17709 Z= 0.317 Chirality : 0.045 0.219 1992 Planarity : 0.004 0.039 2151 Dihedral : 7.580 57.568 2193 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.66 % Allowed : 17.22 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.38 (0.22), residues: 1539 helix: 1.83 (0.21), residues: 642 sheet: 0.24 (0.28), residues: 351 loop : -1.71 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.005 0.001 HIS R 281 PHE 0.010 0.001 PHE G 29 TYR 0.010 0.001 TYR B 32 ARG 0.007 0.001 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 278 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 59 ARG cc_start: 0.8602 (ptt-90) cc_final: 0.8137 (ptt90) REVERT: L 94 MET cc_start: 0.8343 (ptm) cc_final: 0.8056 (ptm) REVERT: H 106 ASN cc_start: 0.8442 (m-40) cc_final: 0.8020 (m-40) REVERT: R 65 TYR cc_start: 0.8490 (t80) cc_final: 0.8232 (t80) REVERT: R 253 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8538 (tt) REVERT: R 272 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.6332 (mp10) REVERT: A 79 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8469 (ptpp) REVERT: B 57 ASN cc_start: 0.8784 (m110) cc_final: 0.8435 (m110) REVERT: B 106 ASN cc_start: 0.8477 (m-40) cc_final: 0.8199 (m110) REVERT: C 132 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8385 (tt) REVERT: C 272 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6410 (mp10) REVERT: G 150 LEU cc_start: 0.9117 (tt) cc_final: 0.8916 (tp) REVERT: G 253 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8554 (tt) REVERT: G 272 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6554 (mp10) outliers start: 63 outliers final: 49 residues processed: 302 average time/residue: 0.2538 time to fit residues: 109.5559 Evaluate side-chains 331 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 275 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain R residue 274 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13023 Z= 0.215 Angle : 0.586 8.605 17709 Z= 0.298 Chirality : 0.044 0.216 1992 Planarity : 0.004 0.039 2151 Dihedral : 7.352 59.691 2193 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.43 % Allowed : 17.74 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.43 (0.22), residues: 1539 helix: 1.88 (0.21), residues: 642 sheet: 0.25 (0.28), residues: 351 loop : -1.69 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.005 0.001 HIS R 281 PHE 0.008 0.001 PHE G 29 TYR 0.011 0.001 TYR H 54 ARG 0.007 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 281 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 94 MET cc_start: 0.8340 (ptm) cc_final: 0.8028 (ptm) REVERT: H 106 ASN cc_start: 0.8463 (m-40) cc_final: 0.8080 (m110) REVERT: R 65 TYR cc_start: 0.8482 (t80) cc_final: 0.8224 (t80) REVERT: R 253 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8513 (tt) REVERT: R 272 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6277 (mp10) REVERT: A 59 ARG cc_start: 0.8229 (ptt90) cc_final: 0.7852 (ptt90) REVERT: A 79 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8474 (ptpp) REVERT: B 57 ASN cc_start: 0.8778 (m110) cc_final: 0.8444 (m110) REVERT: B 106 ASN cc_start: 0.8451 (m-40) cc_final: 0.8179 (m110) REVERT: C 132 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8371 (tt) REVERT: C 272 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6339 (mp10) REVERT: G 150 LEU cc_start: 0.9066 (tt) cc_final: 0.8863 (tp) REVERT: G 195 TRP cc_start: 0.7506 (m100) cc_final: 0.6551 (m-90) REVERT: G 253 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8523 (tt) REVERT: G 272 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6463 (mp10) outliers start: 60 outliers final: 51 residues processed: 304 average time/residue: 0.2668 time to fit residues: 114.9607 Evaluate side-chains 333 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 275 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 HIS Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain R residue 274 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13023 Z= 0.215 Angle : 0.597 9.963 17709 Z= 0.301 Chirality : 0.043 0.218 1992 Planarity : 0.004 0.039 2151 Dihedral : 7.280 57.674 2193 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.80 % Allowed : 17.66 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.43 (0.22), residues: 1539 helix: 1.87 (0.21), residues: 642 sheet: 0.28 (0.28), residues: 351 loop : -1.70 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS R 281 PHE 0.008 0.001 PHE G 29 TYR 0.010 0.001 TYR H 54 ARG 0.008 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 280 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 94 MET cc_start: 0.8377 (ptm) cc_final: 0.8049 (ptm) REVERT: H 106 ASN cc_start: 0.8426 (m-40) cc_final: 0.7983 (m110) REVERT: R 65 TYR cc_start: 0.8476 (t80) cc_final: 0.8223 (t80) REVERT: R 253 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8468 (tt) REVERT: R 272 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6299 (mp10) REVERT: A 79 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8472 (ptpp) REVERT: B 57 ASN cc_start: 0.8760 (m110) cc_final: 0.8422 (m110) REVERT: C 132 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8378 (tt) REVERT: C 272 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6370 (mp10) REVERT: G 195 TRP cc_start: 0.7494 (m100) cc_final: 0.6551 (m-90) REVERT: G 253 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8501 (tt) REVERT: G 272 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6422 (mp10) outliers start: 65 outliers final: 55 residues processed: 308 average time/residue: 0.2539 time to fit residues: 111.5864 Evaluate side-chains 338 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 276 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 HIS Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain R residue 274 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.0020 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 152 optimal weight: 0.0470 chunk 140 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.4886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13023 Z= 0.161 Angle : 0.584 10.901 17709 Z= 0.293 Chirality : 0.043 0.210 1992 Planarity : 0.004 0.039 2151 Dihedral : 7.040 59.746 2193 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.77 % Allowed : 19.22 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.48 (0.22), residues: 1539 helix: 1.96 (0.21), residues: 642 sheet: 0.19 (0.28), residues: 360 loop : -1.68 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.003 0.001 HIS R 281 PHE 0.020 0.001 PHE R 87 TYR 0.011 0.001 TYR H 54 ARG 0.008 0.000 ARG G 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 283 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 94 MET cc_start: 0.8320 (ptm) cc_final: 0.8001 (ptm) REVERT: H 106 ASN cc_start: 0.8376 (m-40) cc_final: 0.7967 (m110) REVERT: R 65 TYR cc_start: 0.8459 (t80) cc_final: 0.8206 (t80) REVERT: R 253 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (tt) REVERT: R 272 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6321 (mp10) REVERT: A 39 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7248 (p0) REVERT: A 59 ARG cc_start: 0.7945 (ptt90) cc_final: 0.7548 (ptt90) REVERT: C 132 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8332 (tt) REVERT: G 195 TRP cc_start: 0.7390 (m100) cc_final: 0.6504 (m-90) REVERT: G 253 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8472 (tt) REVERT: G 272 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6351 (mp10) outliers start: 51 outliers final: 41 residues processed: 308 average time/residue: 0.2583 time to fit residues: 113.2006 Evaluate side-chains 324 residues out of total 1353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 277 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain R residue 274 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 143 ASN Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 GLN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108714 restraints weight = 18195.793| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.52 r_work: 0.3142 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13023 Z= 0.162 Angle : 0.581 10.568 17709 Z= 0.293 Chirality : 0.042 0.205 1992 Planarity : 0.004 0.038 2151 Dihedral : 6.904 58.234 2193 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.40 % Allowed : 19.81 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.51 (0.22), residues: 1539 helix: 2.00 (0.21), residues: 642 sheet: 0.24 (0.28), residues: 360 loop : -1.71 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.002 0.001 HIS R 281 PHE 0.006 0.001 PHE C 189 TYR 0.010 0.001 TYR H 54 ARG 0.008 0.000 ARG G 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2970.12 seconds wall clock time: 54 minutes 53.58 seconds (3293.58 seconds total)