Starting phenix.real_space_refine on Mon Mar 25 17:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/03_2024/8st4_40757_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/03_2024/8st4_40757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/03_2024/8st4_40757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/03_2024/8st4_40757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/03_2024/8st4_40757_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/03_2024/8st4_40757_trim_updated.pdb" } resolution = 2.35 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 132 5.16 5 Na 1 4.78 5 C 16317 2.51 5 N 4102 2.21 5 O 4738 1.98 5 H 24869 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 198": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "I GLU 198": "OE1" <-> "OE2" Residue "K GLU 90": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50159 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "B" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5882 Classifications: {'peptide': 359} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 337} Chain breaks: 1 Chain: "C" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5882 Classifications: {'peptide': 359} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 337} Chain breaks: 1 Chain: "D" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "E" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5882 Classifications: {'peptide': 359} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 337} Chain breaks: 1 Chain: "F" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "H" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "I" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "K" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 22.19, per 1000 atoms: 0.44 Number of scatterers: 50159 At special positions: 0 Unit cell: (143.3, 205.325, 145.438, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 Na 1 11.00 O 4738 8.00 N 4102 7.00 C 16317 6.00 H 24869 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 199 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 202 " 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 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 701 " - " ASN A 31 " " NAG A 702 " - " ASN A 81 " " NAG A 703 " - " ASN A 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 81 " " NAG D 703 " - " ASN D 148 " " NAG L 1 " - " ASN B 143 " " NAG M 1 " - " ASN C 143 " " NAG N 1 " - " ASN E 143 " Time building additional restraints: 39.50 Conformation dependent library (CDL) restraints added in 5.1 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5996 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 52 sheets defined 23.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.492A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.885A pdb=" N LEU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 248 through 267 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 316 through 329 removed outlier: 5.833A pdb=" N VAL A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 342 through 381 Proline residue: A 379 - end of helix Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 210 through 231 removed outlier: 4.223A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix removed outlier: 3.647A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 240 through 261 Processing helix chain 'B' and resid 271 through 297 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 338 through 363 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.627A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.795A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 240 through 261 Processing helix chain 'C' and resid 271 through 297 Processing helix chain 'C' and resid 308 through 314 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 338 through 362 Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 218 through 234 removed outlier: 4.537A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.936A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 248 through 267 Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 316 through 329 removed outlier: 5.756A pdb=" N VAL D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 342 through 381 Proline residue: D 379 - end of helix Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.492A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix removed outlier: 3.723A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 271 through 297 Processing helix chain 'E' and resid 308 through 322 removed outlier: 5.436A pdb=" N LEU E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Proline residue: E 319 - end of helix Processing helix chain 'E' and resid 338 through 362 Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 188 through 191 No H-bonds generated for 'chain 'F' and resid 188 through 191' Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 192 through 197 Proline residue: G 196 - end of helix No H-bonds generated for 'chain 'G' and resid 192 through 197' Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'I' and resid 192 through 195 No H-bonds generated for 'chain 'I' and resid 192 through 195' Processing helix chain 'J' and resid 85 through 87 No H-bonds generated for 'chain 'J' and resid 85 through 87' Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 155 through 157 No H-bonds generated for 'chain 'J' and resid 155 through 157' Processing helix chain 'J' and resid 188 through 192 Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 192 through 195 No H-bonds generated for 'chain 'K' and resid 192 through 195' Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 5.988A pdb=" N VAL A 36 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A 166 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 38 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'A' and resid 84 through 87 Processing sheet with id= D, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.464A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.468A pdb=" N VAL B 31 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 33 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 32 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU B 63 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN B 55 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= G, first strand: chain 'B' and resid 79 through 83 Processing sheet with id= H, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.128A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 178 through 182 removed outlier: 6.764A pdb=" N ILE B 204 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.309A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= L, first strand: chain 'C' and resid 79 through 83 Processing sheet with id= M, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.899A pdb=" N ARG C 206 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE C 180 " --> pdb=" O ARG C 206 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.125A pdb=" N VAL D 36 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL D 166 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 38 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= P, first strand: chain 'D' and resid 84 through 88 Processing sheet with id= Q, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.371A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 189 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 158 through 162 removed outlier: 6.514A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 44 through 46 Processing sheet with id= T, first strand: chain 'E' and resid 79 through 83 Processing sheet with id= U, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.224A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 178 through 182 removed outlier: 6.746A pdb=" N ILE E 204 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 4 through 7 Processing sheet with id= X, first strand: chain 'F' and resid 90 through 92 removed outlier: 6.023A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.873A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.530A pdb=" N ASN F 150 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 196 through 198 Processing sheet with id= AB, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.051A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.544A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS G 39 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG G 48 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ARG G 41 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU G 46 " --> pdb=" O ARG G 41 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 127 through 130 Processing sheet with id= AE, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.534A pdb=" N VAL G 143 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 158 through 160 Processing sheet with id= AG, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= AH, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.088A pdb=" N LYS H 108 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU H 42 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU H 51 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.549A pdb=" N ASN H 142 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 149 through 152 removed outlier: 3.794A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= AL, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.555A pdb=" N GLY I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS I 39 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG I 48 " --> pdb=" O LYS I 39 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 142 through 144 removed outlier: 3.802A pdb=" N VAL I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 158 through 161 removed outlier: 4.319A pdb=" N CYS I 202 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS I 215 " --> pdb=" O CYS I 202 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 170 through 172 removed outlier: 3.556A pdb=" N SER I 187 " --> pdb=" O HIS I 171 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU I 184 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS I 150 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER I 186 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU I 148 " --> pdb=" O SER I 186 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'J' and resid 4 through 7 Processing sheet with id= AQ, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.211A pdb=" N LYS J 108 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY J 89 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU J 42 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU J 51 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 119 through 123 Processing sheet with id= AS, first strand: chain 'J' and resid 153 through 155 removed outlier: 4.494A pdb=" N TRP J 153 " --> pdb=" O ARG J 160 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 196 through 198 Processing sheet with id= AU, first strand: chain 'J' and resid 141 through 144 removed outlier: 6.085A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'K' and resid 4 through 7 Processing sheet with id= AW, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.637A pdb=" N GLY K 50 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LYS K 39 " --> pdb=" O ARG K 48 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ARG K 48 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.916A pdb=" N GLY K 146 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'K' and resid 142 through 144 removed outlier: 3.523A pdb=" N VAL K 143 " --> pdb=" O VAL K 190 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 203 through 206 940 hydrogen bonds defined for protein. 2628 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: 19.30 Time building geometry restraints manager: 41.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 24844 1.02 - 1.22: 44 1.22 - 1.43: 10950 1.43 - 1.63: 14787 1.63 - 1.84: 201 Bond restraints: 50826 Sorted by residual: bond pdb=" NE ARG C 155 " pdb=" HE ARG C 155 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" N ASN B 97 " pdb=" CA ASN B 97 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.32e-02 5.74e+03 7.90e+00 bond pdb=" C ARG C 155 " pdb=" O ARG C 155 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.29e-02 6.01e+03 7.84e+00 bond pdb=" N ASP B 99 " pdb=" CA ASP B 99 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.06e-02 8.90e+03 7.59e+00 bond pdb=" C ILE B 51 " pdb=" O ILE B 51 " ideal model delta sigma weight residual 1.236 1.208 0.027 1.00e-02 1.00e+04 7.44e+00 ... (remaining 50821 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.27: 474 104.27 - 111.82: 58125 111.82 - 119.36: 12085 119.36 - 126.90: 20676 126.90 - 134.44: 482 Bond angle restraints: 91842 Sorted by residual: angle pdb=" N ASP G 180 " pdb=" CA ASP G 180 " pdb=" C ASP G 180 " ideal model delta sigma weight residual 114.56 107.89 6.67 1.27e+00 6.20e-01 2.76e+01 angle pdb=" C TYR J 145 " pdb=" N PRO J 146 " pdb=" CD PRO J 146 " ideal model delta sigma weight residual 120.60 111.75 8.85 2.20e+00 2.07e-01 1.62e+01 angle pdb=" CA ASN B 97 " pdb=" C ASN B 97 " pdb=" O ASN B 97 " ideal model delta sigma weight residual 121.87 117.50 4.37 1.10e+00 8.26e-01 1.58e+01 angle pdb=" CA SER C 113 " pdb=" C SER C 113 " pdb=" O SER C 113 " ideal model delta sigma weight residual 121.72 117.17 4.55 1.18e+00 7.18e-01 1.48e+01 angle pdb=" CA ILE C 43 " pdb=" C ILE C 43 " pdb=" O ILE C 43 " ideal model delta sigma weight residual 121.17 117.49 3.68 1.06e+00 8.90e-01 1.21e+01 ... (remaining 91837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.01: 22737 22.01 - 44.01: 1324 44.01 - 66.02: 274 66.02 - 88.02: 65 88.02 - 110.03: 13 Dihedral angle restraints: 24413 sinusoidal: 13192 harmonic: 11221 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual 93.00 158.99 -65.99 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS E 130 " pdb=" SG CYS E 130 " pdb=" SG CYS E 144 " pdb=" CB CYS E 144 " ideal model delta sinusoidal sigma weight residual 93.00 36.39 56.61 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 149.15 -56.15 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 24410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3737 0.082 - 0.164: 354 0.164 - 0.246: 3 0.246 - 0.328: 3 0.328 - 0.411: 1 Chirality restraints: 4098 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 81 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4095 not shown) Planarity restraints: 7336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 97 " -0.137 2.00e-02 2.50e+03 1.48e-01 3.29e+02 pdb=" CG ASN B 97 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 97 " 0.132 2.00e-02 2.50e+03 pdb=" ND2 ASN B 97 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 97 " -0.222 2.00e-02 2.50e+03 pdb="HD22 ASN B 97 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR J 145 " 0.081 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PRO J 146 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO J 146 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO J 146 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 81 " -0.042 2.00e-02 2.50e+03 3.44e-02 1.78e+01 pdb=" CG ASN A 81 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 81 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 81 " 0.038 2.00e-02 2.50e+03 pdb="HD21 ASN A 81 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.052 2.00e-02 2.50e+03 ... (remaining 7333 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 92 1.80 - 2.50: 37235 2.50 - 3.20: 151658 3.20 - 3.90: 205722 3.90 - 4.60: 322034 Nonbonded interactions: 716741 Sorted by model distance: nonbonded pdb=" O PRO B 234 " pdb=" HG CYS B 237 " model vdw 1.103 2.620 nonbonded pdb=" HH TYR E 95 " pdb=" HA TRP E 151 " model vdw 1.435 2.270 nonbonded pdb=" OE1 GLU F 86 " pdb=" H GLU F 86 " model vdw 1.475 1.850 nonbonded pdb=" HH TYR B 196 " pdb=" OD2 ASP B 198 " model vdw 1.482 1.850 nonbonded pdb=" HD1 HIS J 203 " pdb=" OG1 THR J 205 " model vdw 1.597 1.850 ... (remaining 716736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 1 through 365) selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.760 Extract box with map and model: 8.470 Check model and map are aligned: 0.800 Set scattering table: 0.420 Process input model: 154.090 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.004 0.048 25957 Z= 0.277 Angle : 0.579 9.371 35403 Z= 0.305 Chirality : 0.046 0.411 4098 Planarity : 0.004 0.124 4377 Dihedral : 15.892 110.029 9566 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.03 % Allowed : 14.08 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.04 (0.15), residues: 3115 helix: 1.76 (0.20), residues: 668 sheet: -0.25 (0.16), residues: 1000 loop : -0.51 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 69 HIS 0.004 0.001 HIS E 329 PHE 0.018 0.001 PHE C 254 TYR 0.017 0.002 TYR E 95 ARG 0.007 0.001 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 2.9215 time to fit residues: 916.8990 Evaluate side-chains 233 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 9.9990 chunk 231 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 155 optimal weight: 0.0570 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN F 27 GLN F 171 GLN G 60 ASN H 143 ASN ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN J 171 GLN ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25957 Z= 0.164 Angle : 0.516 5.731 35403 Z= 0.270 Chirality : 0.043 0.164 4098 Planarity : 0.004 0.071 4377 Dihedral : 6.804 69.318 3709 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.98 % Allowed : 14.25 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.28 (0.15), residues: 3115 helix: 2.18 (0.20), residues: 657 sheet: -0.18 (0.16), residues: 1003 loop : -0.40 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 62 HIS 0.003 0.001 HIS D 9 PHE 0.012 0.001 PHE C 254 TYR 0.014 0.001 TYR E 344 ARG 0.007 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 4.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: C 36 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7752 (tpp) outliers start: 28 outliers final: 9 residues processed: 268 average time/residue: 2.7819 time to fit residues: 872.1653 Evaluate side-chains 243 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 232 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 24 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 171 GLN G 60 ASN J 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25957 Z= 0.196 Angle : 0.507 6.474 35403 Z= 0.263 Chirality : 0.043 0.151 4098 Planarity : 0.004 0.065 4377 Dihedral : 5.303 43.233 3709 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.22 % Allowed : 13.55 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.31 (0.15), residues: 3115 helix: 2.21 (0.20), residues: 657 sheet: -0.17 (0.16), residues: 1002 loop : -0.38 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 62 HIS 0.002 0.001 HIS B 297 PHE 0.015 0.001 PHE C 254 TYR 0.015 0.001 TYR K 105 ARG 0.012 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 247 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: J 18 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6468 (tt0) outliers start: 35 outliers final: 15 residues processed: 270 average time/residue: 2.6531 time to fit residues: 844.6053 Evaluate side-chains 254 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 237 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 142 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 294 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 263 optimal weight: 8.9990 chunk 79 optimal weight: 0.0370 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25957 Z= 0.249 Angle : 0.528 6.838 35403 Z= 0.276 Chirality : 0.044 0.151 4098 Planarity : 0.004 0.070 4377 Dihedral : 4.923 30.856 3709 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.43 % Allowed : 13.94 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.18 (0.15), residues: 3115 helix: 1.91 (0.20), residues: 675 sheet: -0.16 (0.16), residues: 1008 loop : -0.45 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 101 HIS 0.003 0.001 HIS E 136 PHE 0.017 0.001 PHE C 254 TYR 0.014 0.001 TYR G 104 ARG 0.014 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 236 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: E 63 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: G 81 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: H 32 SER cc_start: 0.4967 (OUTLIER) cc_final: 0.4597 (p) REVERT: J 38 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8474 (tp) outliers start: 41 outliers final: 23 residues processed: 263 average time/residue: 2.6325 time to fit residues: 822.3712 Evaluate side-chains 259 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 81 TYR Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 142 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 219 optimal weight: 0.1980 chunk 121 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25957 Z= 0.140 Angle : 0.477 7.082 35403 Z= 0.247 Chirality : 0.042 0.142 4098 Planarity : 0.004 0.077 4377 Dihedral : 4.470 23.089 3709 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.19 % Allowed : 14.25 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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 (0.15), residues: 3115 helix: 2.30 (0.20), residues: 655 sheet: -0.11 (0.16), residues: 1039 loop : -0.36 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 101 HIS 0.003 0.001 HIS E 297 PHE 0.016 0.001 PHE I 173 TYR 0.013 0.001 TYR K 105 ARG 0.014 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 4.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: E 63 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: G 81 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: J 18 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6460 (tt0) outliers start: 34 outliers final: 17 residues processed: 265 average time/residue: 2.7274 time to fit residues: 848.2008 Evaluate side-chains 259 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 238 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 81 TYR Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 142 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 60 ASN ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25957 Z= 0.296 Angle : 0.541 6.688 35403 Z= 0.284 Chirality : 0.044 0.154 4098 Planarity : 0.004 0.064 4377 Dihedral : 4.767 32.690 3709 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.40 % Allowed : 14.04 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.19 (0.15), residues: 3115 helix: 1.91 (0.20), residues: 673 sheet: -0.13 (0.16), residues: 1041 loop : -0.48 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 101 HIS 0.003 0.001 HIS B 86 PHE 0.019 0.002 PHE C 254 TYR 0.013 0.002 TYR D 100 ARG 0.011 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: E 63 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: H 32 SER cc_start: 0.4984 (OUTLIER) cc_final: 0.4679 (p) REVERT: J 18 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6479 (tt0) REVERT: J 38 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8469 (tp) outliers start: 40 outliers final: 23 residues processed: 262 average time/residue: 2.7927 time to fit residues: 861.9747 Evaluate side-chains 261 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 233 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 168 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 179 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25957 Z= 0.159 Angle : 0.489 7.536 35403 Z= 0.253 Chirality : 0.042 0.144 4098 Planarity : 0.004 0.071 4377 Dihedral : 4.524 25.579 3709 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.98 % Allowed : 14.60 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.30 (0.15), residues: 3115 helix: 2.05 (0.20), residues: 673 sheet: -0.09 (0.16), residues: 1039 loop : -0.41 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 168 HIS 0.003 0.001 HIS E 297 PHE 0.016 0.001 PHE I 173 TYR 0.013 0.001 TYR G 104 ARG 0.011 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 240 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: E 63 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: G 81 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: H 32 SER cc_start: 0.4961 (OUTLIER) cc_final: 0.4591 (p) outliers start: 28 outliers final: 19 residues processed: 260 average time/residue: 2.7404 time to fit residues: 851.4538 Evaluate side-chains 260 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 237 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 81 TYR Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 8.9990 chunk 117 optimal weight: 0.0970 chunk 175 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 GLN ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25957 Z= 0.174 Angle : 0.488 8.311 35403 Z= 0.252 Chirality : 0.042 0.148 4098 Planarity : 0.004 0.083 4377 Dihedral : 4.446 25.694 3709 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.19 % Allowed : 14.39 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.39 (0.15), residues: 3115 helix: 2.24 (0.20), residues: 661 sheet: -0.06 (0.16), residues: 1039 loop : -0.36 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 168 HIS 0.003 0.001 HIS E 297 PHE 0.017 0.001 PHE I 173 TYR 0.011 0.001 TYR E 275 ARG 0.012 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 4.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: E 63 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: G 81 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: H 32 SER cc_start: 0.5030 (OUTLIER) cc_final: 0.4661 (p) REVERT: J 38 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8433 (tp) outliers start: 34 outliers final: 21 residues processed: 268 average time/residue: 2.7458 time to fit residues: 864.1551 Evaluate side-chains 268 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 81 TYR Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 142 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25957 Z= 0.266 Angle : 0.532 8.493 35403 Z= 0.277 Chirality : 0.044 0.152 4098 Planarity : 0.004 0.079 4377 Dihedral : 4.684 27.660 3709 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.05 % Allowed : 14.53 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.25 (0.15), residues: 3115 helix: 1.96 (0.20), residues: 673 sheet: -0.07 (0.16), residues: 1041 loop : -0.45 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 101 HIS 0.004 0.001 HIS B 86 PHE 0.018 0.002 PHE C 254 TYR 0.015 0.002 TYR E 275 ARG 0.012 0.001 ARG I 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 4.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: E 63 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: H 32 SER cc_start: 0.5074 (OUTLIER) cc_final: 0.4748 (p) REVERT: J 38 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8461 (tp) outliers start: 30 outliers final: 22 residues processed: 260 average time/residue: 2.8777 time to fit residues: 882.4273 Evaluate side-chains 262 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 142 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 1.9990 chunk 289 optimal weight: 0.0770 chunk 176 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 279 optimal weight: 0.0020 chunk 241 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.6748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 25957 Z= 0.217 Angle : 0.653 59.200 35403 Z= 0.365 Chirality : 0.043 0.228 4098 Planarity : 0.004 0.079 4377 Dihedral : 4.677 27.485 3709 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.05 % Allowed : 14.53 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.25 (0.15), residues: 3115 helix: 1.95 (0.20), residues: 673 sheet: -0.08 (0.16), residues: 1041 loop : -0.44 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.003 0.001 HIS B 86 PHE 0.018 0.001 PHE C 254 TYR 0.012 0.001 TYR G 104 ARG 0.009 0.000 ARG H 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: E 63 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: H 32 SER cc_start: 0.5060 (OUTLIER) cc_final: 0.4736 (p) REVERT: J 38 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8453 (tp) outliers start: 30 outliers final: 23 residues processed: 259 average time/residue: 2.7161 time to fit residues: 828.0368 Evaluate side-chains 267 residues out of total 2863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 142 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 40.0000 chunk 257 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 223 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 248 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102950 restraints weight = 83373.096| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.20 r_work: 0.2970 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 25957 Z= 0.217 Angle : 0.653 59.200 35403 Z= 0.365 Chirality : 0.043 0.228 4098 Planarity : 0.004 0.079 4377 Dihedral : 4.677 27.485 3709 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.94 % Allowed : 14.74 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % 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: 0.25 (0.15), residues: 3115 helix: 1.95 (0.20), residues: 673 sheet: -0.08 (0.16), residues: 1041 loop : -0.44 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.003 0.001 HIS B 86 PHE 0.018 0.001 PHE C 254 TYR 0.012 0.001 TYR G 104 ARG 0.009 0.000 ARG H 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16090.74 seconds wall clock time: 282 minutes 24.68 seconds (16944.68 seconds total)