Starting phenix.real_space_refine on Sun Feb 25 09:25:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/02_2024/8st3_40756_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/02_2024/8st3_40756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/02_2024/8st3_40756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/02_2024/8st3_40756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/02_2024/8st3_40756_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st3_40756/02_2024/8st3_40756_trim_updated.pdb" } resolution = 2.93 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= 0.008 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 S 135 5.16 5 Na 1 4.78 5 C 16377 2.51 5 N 4096 2.21 5 O 4753 1.98 5 H 24962 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 198": "OE1" <-> "OE2" Residue "J GLU 86": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50327 Number of models: 1 Model: "" Number of chains: 20 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: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5937 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5937 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 340} 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: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5937 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 340} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Unusual residues: {' CA': 2, 'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 53 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 20.19, per 1000 atoms: 0.40 Number of scatterers: 50327 At special positions: 0 Unit cell: (149.716, 198.908, 144.369, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 135 16.00 Na 1 11.00 O 4753 8.00 N 4096 7.00 C 16377 6.00 H 24962 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=2.03 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: 41.55 Conformation dependent library (CDL) restraints added in 5.1 seconds 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 53 sheets defined 23.9% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.94 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: 4.649A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.870A 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 248 through 268 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 316 through 329 removed outlier: 5.750A 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 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: 4.368A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix removed outlier: 3.633A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.857A 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 321 Processing helix chain 'B' and resid 338 through 369 removed outlier: 3.605A pdb=" N THR B 365 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 71 through 74 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: 4.550A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.863A 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 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 322 Processing helix chain 'C' and resid 338 through 368 removed outlier: 4.146A pdb=" N ILE C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) 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 218 through 234 removed outlier: 4.476A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.918A 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: 5.646A 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: 4.486A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix removed outlier: 3.677A 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 313 Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 338 through 365 removed outlier: 4.387A pdb=" N THR E 365 " --> pdb=" O CYS E 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' 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 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 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' 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 36 through 40 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 88 Processing sheet with id= D, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.436A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 189 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 41 through 47 removed outlier: 6.612A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.467A pdb=" N VAL B 31 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 33 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR B 32 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU B 63 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 55 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= H, first strand: chain 'B' and resid 79 through 83 Processing sheet with id= I, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.041A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 178 through 182 removed outlier: 6.929A pdb=" N ILE B 204 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.300A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= M, first strand: chain 'C' and resid 79 through 83 Processing sheet with id= N, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.150A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.834A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.211A pdb=" N VAL D 36 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL D 166 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL D 38 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= R, first strand: chain 'D' and resid 84 through 88 Processing sheet with id= S, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.432A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 189 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 158 through 162 removed outlier: 6.636A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 44 through 46 Processing sheet with id= V, first strand: chain 'E' and resid 79 through 83 Processing sheet with id= W, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.215A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG E 206 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE E 180 " --> pdb=" O ARG E 206 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 4 through 7 Processing sheet with id= Y, first strand: chain 'F' and resid 90 through 92 removed outlier: 6.003A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.757A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER F 179 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER F 167 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.581A pdb=" N ASN F 150 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 196 through 198 Processing sheet with id= AC, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.048A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.386A 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: 7.852A pdb=" N ARG G 41 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU G 46 " --> pdb=" O ARG G 41 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 127 through 130 Processing sheet with id= AF, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.678A pdb=" N VAL G 143 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 158 through 160 Processing sheet with id= AH, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= AI, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.148A pdb=" N LYS H 108 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU H 42 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU H 51 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.578A pdb=" N ASN H 142 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H 179 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER H 167 " --> pdb=" O SER H 181 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 149 through 152 removed outlier: 3.756A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.529A pdb=" N THR I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.550A pdb=" N GLY I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS I 39 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG I 48 " --> pdb=" O LYS I 39 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 142 through 144 removed outlier: 3.717A pdb=" N VAL I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 158 through 161 removed outlier: 4.285A pdb=" N CYS I 202 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS I 215 " --> pdb=" O CYS I 202 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 170 through 172 removed outlier: 3.525A pdb=" N SER I 187 " --> pdb=" O HIS I 171 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU I 184 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS I 150 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER I 186 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU I 148 " --> pdb=" O SER I 186 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 4 through 7 Processing sheet with id= AR, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.190A pdb=" N LYS J 108 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY J 89 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU J 42 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU J 51 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'J' and resid 119 through 123 Processing sheet with id= AT, first strand: chain 'J' and resid 153 through 155 removed outlier: 4.455A pdb=" N TRP J 153 " --> pdb=" O ARG J 160 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'J' and resid 196 through 201 Processing sheet with id= AV, first strand: chain 'J' and resid 141 through 144 removed outlier: 6.210A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 4 through 7 Processing sheet with id= AX, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.565A pdb=" N GLY K 50 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS K 39 " --> pdb=" O ARG K 48 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ARG K 48 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.979A pdb=" N GLY K 146 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 142 through 144 removed outlier: 3.585A pdb=" N VAL K 143 " --> pdb=" O VAL K 190 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 203 through 206 956 hydrogen bonds defined for protein. 2676 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: 20.39 Time building geometry restraints manager: 41.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 24937 1.04 - 1.24: 2578 1.24 - 1.43: 8748 1.43 - 1.63: 14521 1.63 - 1.83: 207 Bond restraints: 50991 Sorted by residual: bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASP J 1 " pdb=" CA ASP J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" N ASP H 1 " pdb=" CA ASP H 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.59e+00 bond pdb=" N ASP H 1 " pdb=" H ASP H 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" N ASP F 1 " pdb=" H ASP F 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 ... (remaining 50986 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.75: 987 106.75 - 113.58: 60898 113.58 - 120.41: 15693 120.41 - 127.24: 14184 127.24 - 134.07: 401 Bond angle restraints: 92163 Sorted by residual: angle pdb=" N SER I 179 " pdb=" CA SER I 179 " pdb=" C SER I 179 " ideal model delta sigma weight residual 112.72 108.96 3.76 1.28e+00 6.10e-01 8.64e+00 angle pdb=" C ASP B 193 " pdb=" N SER B 194 " pdb=" CA SER B 194 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.45e+00 angle pdb=" N SER K 179 " pdb=" CA SER K 179 " pdb=" C SER K 179 " ideal model delta sigma weight residual 112.93 109.43 3.50 1.33e+00 5.65e-01 6.94e+00 angle pdb=" N ASP A 104 " pdb=" CA ASP A 104 " pdb=" CB ASP A 104 " ideal model delta sigma weight residual 112.47 108.65 3.82 1.52e+00 4.33e-01 6.32e+00 angle pdb=" C PRO E 90 " pdb=" N ASP E 91 " pdb=" CA ASP E 91 " ideal model delta sigma weight residual 122.21 118.56 3.65 1.48e+00 4.57e-01 6.09e+00 ... (remaining 92158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 22762 21.90 - 43.80: 1356 43.80 - 65.69: 294 65.69 - 87.59: 67 87.59 - 109.49: 15 Dihedral angle restraints: 24494 sinusoidal: 13246 harmonic: 11248 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 -86.00 -173.56 87.56 1 1.00e+01 1.00e-02 9.19e+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 93.00 147.72 -54.72 1 1.00e+01 1.00e-02 4.05e+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 42.32 50.68 1 1.00e+01 1.00e-02 3.52e+01 ... (remaining 24491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3334 0.052 - 0.104: 627 0.104 - 0.156: 149 0.156 - 0.208: 0 0.208 - 0.261: 3 Chirality restraints: 4113 Sorted by residual: 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 1.70e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.53e+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 -2.51 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4110 not shown) Planarity restraints: 7357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 326 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.24e+00 pdb=" N PRO C 327 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 180 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ILE C 180 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE C 180 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL C 181 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 307 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO E 308 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 308 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 308 " -0.028 5.00e-02 4.00e+02 ... (remaining 7354 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 750 2.07 - 2.70: 79993 2.70 - 3.33: 145928 3.33 - 3.97: 193692 3.97 - 4.60: 301066 Nonbonded interactions: 721429 Sorted by model distance: nonbonded pdb="HD21 ASN H 166 " pdb=" HZ3 TRP H 168 " model vdw 1.432 2.100 nonbonded pdb=" OE1 GLU K 90 " pdb=" H GLU K 90 " model vdw 1.488 1.850 nonbonded pdb=" OE1 GLU F 86 " pdb=" H GLU F 86 " model vdw 1.536 1.850 nonbonded pdb=" O GLN J 129 " pdb="HE21 GLN J 129 " model vdw 1.552 1.850 nonbonded pdb=" HD2 TYR D 197 " pdb=" OD2 ASP E 171 " model vdw 1.566 2.450 ... (remaining 721424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 383 or resid 701 through 705)) selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 1 through 372) 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: 2.110 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: 0.720 Extract box with map and model: 8.360 Check model and map are aligned: 0.720 Set scattering table: 0.420 Process input model: 152.750 Find NCS groups from input model: 2.410 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.005 0.044 26029 Z= 0.310 Angle : 0.554 7.287 35502 Z= 0.282 Chirality : 0.044 0.261 4113 Planarity : 0.004 0.075 4389 Dihedral : 15.963 109.490 9596 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.07 % Allowed : 14.55 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.15 (0.15), residues: 3127 helix: 1.74 (0.20), residues: 670 sheet: -0.14 (0.16), residues: 1016 loop : -0.41 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 101 HIS 0.005 0.001 HIS D 305 PHE 0.011 0.001 PHE B 278 TYR 0.032 0.001 TYR E 95 ARG 0.011 0.001 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 338 time to evaluate : 4.372 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.7336 (t0) cc_final: 0.7098 (t0) REVERT: B 368 MET cc_start: 0.3868 (tmm) cc_final: 0.3512 (mmp) REVERT: C 95 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8961 (m-80) REVERT: F 11 LEU cc_start: 0.7949 (tp) cc_final: 0.7633 (tt) REVERT: F 35 ASN cc_start: 0.6346 (m110) cc_final: 0.6086 (m-40) REVERT: F 66 ARG cc_start: 0.7902 (ptt-90) cc_final: 0.7471 (ptt-90) REVERT: F 84 GLU cc_start: 0.7464 (mp0) cc_final: 0.7086 (mp0) REVERT: F 178 TYR cc_start: 0.7413 (m-80) cc_final: 0.7171 (m-80) REVERT: G 158 THR cc_start: 0.8918 (m) cc_final: 0.8644 (p) REVERT: H 11 LEU cc_start: 0.8408 (tp) cc_final: 0.8066 (tt) REVERT: H 24 ARG cc_start: 0.6891 (mtp-110) cc_final: 0.6527 (ttm110) REVERT: I 155 GLU cc_start: 0.8976 (mp0) cc_final: 0.8672 (OUTLIER) REVERT: J 58 ASN cc_start: 0.8542 (m110) cc_final: 0.8316 (m-40) REVERT: J 84 GLU cc_start: 0.7231 (tt0) cc_final: 0.6403 (tm-30) outliers start: 2 outliers final: 3 residues processed: 340 average time/residue: 2.7067 time to fit residues: 1082.0313 Evaluate side-chains 261 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain F residue 65 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN G 4 GLN G 6 GLN G 60 ASN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26029 Z= 0.288 Angle : 0.543 6.233 35502 Z= 0.279 Chirality : 0.044 0.160 4113 Planarity : 0.004 0.067 4389 Dihedral : 6.396 63.324 3724 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.43 % Allowed : 15.60 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 3127 helix: 1.99 (0.20), residues: 677 sheet: -0.25 (0.16), residues: 996 loop : -0.41 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.004 0.001 HIS E 297 PHE 0.014 0.001 PHE H 140 TYR 0.013 0.001 TYR G 104 ARG 0.008 0.000 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 254 time to evaluate : 4.118 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 MET cc_start: 0.4093 (tmm) cc_final: 0.3572 (mmp) REVERT: C 95 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.9033 (m-80) REVERT: D 364 MET cc_start: 0.8123 (ttm) cc_final: 0.7827 (ttt) REVERT: E 95 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.6951 (m-10) REVERT: E 359 PHE cc_start: 0.7811 (m-10) cc_final: 0.7551 (m-10) REVERT: F 4 MET cc_start: 0.7454 (mmm) cc_final: 0.6929 (mmm) REVERT: F 66 ARG cc_start: 0.7896 (ptt-90) cc_final: 0.7253 (ptt-90) REVERT: F 82 ARG cc_start: 0.7695 (ttp-110) cc_final: 0.6993 (mpp80) REVERT: F 84 GLU cc_start: 0.7318 (mp0) cc_final: 0.6338 (mp0) REVERT: F 180 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5473 (tpt) REVERT: G 158 THR cc_start: 0.8935 (m) cc_final: 0.8663 (p) REVERT: H 11 LEU cc_start: 0.8439 (tp) cc_final: 0.8106 (tt) REVERT: H 24 ARG cc_start: 0.7142 (mtp-110) cc_final: 0.6593 (ttm110) REVERT: I 155 GLU cc_start: 0.8933 (mp0) cc_final: 0.8693 (OUTLIER) REVERT: I 181 LEU cc_start: 0.9346 (mm) cc_final: 0.9045 (mm) REVERT: J 32 SER cc_start: 0.6571 (OUTLIER) cc_final: 0.5824 (p) outliers start: 41 outliers final: 22 residues processed: 280 average time/residue: 2.5578 time to fit residues: 850.3209 Evaluate side-chains 270 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 280 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 277 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26029 Z= 0.200 Angle : 0.498 6.122 35502 Z= 0.253 Chirality : 0.043 0.149 4113 Planarity : 0.004 0.070 4389 Dihedral : 5.091 50.321 3722 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.29 % Allowed : 15.84 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 3127 helix: 2.15 (0.20), residues: 677 sheet: -0.24 (0.16), residues: 1000 loop : -0.37 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 101 HIS 0.003 0.001 HIS E 297 PHE 0.020 0.001 PHE J 214 TYR 0.013 0.001 TYR F 191 ARG 0.009 0.000 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 4.019 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.9082 (mtm) cc_final: 0.8865 (ttm) REVERT: B 321 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8639 (mp) REVERT: B 368 MET cc_start: 0.4097 (tmm) cc_final: 0.3584 (mmp) REVERT: C 95 TYR cc_start: 0.9344 (OUTLIER) cc_final: 0.8983 (m-80) REVERT: D 56 MET cc_start: 0.8915 (mtp) cc_final: 0.8411 (mtt) REVERT: D 364 MET cc_start: 0.8103 (ttm) cc_final: 0.7823 (ttt) REVERT: E 95 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.6908 (m-10) REVERT: F 4 MET cc_start: 0.7592 (mmm) cc_final: 0.7058 (mmm) REVERT: F 66 ARG cc_start: 0.7865 (ptt-90) cc_final: 0.7457 (ptt-90) REVERT: F 82 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7364 (ttp-110) REVERT: F 84 GLU cc_start: 0.7389 (mp0) cc_final: 0.6722 (mp0) REVERT: H 11 LEU cc_start: 0.8417 (tp) cc_final: 0.8062 (tt) REVERT: H 24 ARG cc_start: 0.7169 (mtp-110) cc_final: 0.6490 (ttm110) REVERT: H 87 ASP cc_start: 0.7889 (m-30) cc_final: 0.7653 (m-30) REVERT: H 149 ILE cc_start: 0.6609 (tt) cc_final: 0.6224 (tp) REVERT: H 195 ASN cc_start: 0.7456 (p0) cc_final: 0.7207 (p0) REVERT: H 216 ARG cc_start: 0.6251 (tpm-80) cc_final: 0.5996 (tpm-80) REVERT: I 155 GLU cc_start: 0.8904 (mp0) cc_final: 0.8676 (mp0) outliers start: 37 outliers final: 23 residues processed: 277 average time/residue: 2.7174 time to fit residues: 888.5483 Evaluate side-chains 266 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 240 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 0.0040 chunk 133 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 281 optimal weight: 20.0000 chunk 297 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 266 optimal weight: 0.0970 chunk 80 optimal weight: 0.0980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 143 ASN J 129 GLN ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 26029 Z= 0.147 Angle : 0.473 5.788 35502 Z= 0.241 Chirality : 0.042 0.159 4113 Planarity : 0.004 0.071 4389 Dihedral : 4.480 50.532 3722 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 1.39 % Allowed : 15.53 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 3127 helix: 2.29 (0.20), residues: 677 sheet: -0.21 (0.16), residues: 999 loop : -0.30 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 101 HIS 0.003 0.000 HIS E 297 PHE 0.016 0.001 PHE H 140 TYR 0.012 0.001 TYR F 145 ARG 0.008 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 246 time to evaluate : 4.514 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8772 (ttt) REVERT: B 77 MET cc_start: 0.9115 (mtm) cc_final: 0.8907 (ttm) REVERT: B 321 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8594 (mp) REVERT: B 368 MET cc_start: 0.3883 (tmm) cc_final: 0.3462 (mmp) REVERT: C 95 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.8978 (m-80) REVERT: D 56 MET cc_start: 0.8855 (mtp) cc_final: 0.8323 (mtt) REVERT: D 364 MET cc_start: 0.8076 (ttm) cc_final: 0.7786 (ttt) REVERT: E 95 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.6893 (m-10) REVERT: F 4 MET cc_start: 0.7724 (mmm) cc_final: 0.7164 (mmm) REVERT: F 66 ARG cc_start: 0.7838 (ptt-90) cc_final: 0.7594 (ptt-90) REVERT: F 84 GLU cc_start: 0.7414 (mp0) cc_final: 0.7023 (mp0) REVERT: F 168 TRP cc_start: 0.8571 (OUTLIER) cc_final: 0.7702 (m-90) REVERT: H 11 LEU cc_start: 0.8408 (tp) cc_final: 0.8046 (tt) REVERT: H 24 ARG cc_start: 0.7108 (mtp-110) cc_final: 0.6613 (ttm110) REVERT: H 87 ASP cc_start: 0.7954 (m-30) cc_final: 0.7705 (m-30) REVERT: H 149 ILE cc_start: 0.6430 (tt) cc_final: 0.6154 (tp) REVERT: H 180 MET cc_start: 0.6863 (tpp) cc_final: 0.6398 (tpt) REVERT: I 155 GLU cc_start: 0.8942 (mp0) cc_final: 0.8674 (OUTLIER) REVERT: J 32 SER cc_start: 0.6841 (OUTLIER) cc_final: 0.6299 (p) REVERT: J 216 ARG cc_start: 0.6481 (ttp80) cc_final: 0.5876 (tpm170) outliers start: 40 outliers final: 18 residues processed: 276 average time/residue: 2.7000 time to fit residues: 890.3749 Evaluate side-chains 255 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 168 TRP Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 221 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 195 ASN ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26029 Z= 0.164 Angle : 0.475 10.343 35502 Z= 0.241 Chirality : 0.042 0.200 4113 Planarity : 0.004 0.050 4389 Dihedral : 4.302 50.602 3722 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 1.22 % Allowed : 15.74 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.44 (0.15), residues: 3127 helix: 2.36 (0.20), residues: 677 sheet: -0.17 (0.16), residues: 999 loop : -0.28 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 101 HIS 0.003 0.001 HIS B 297 PHE 0.010 0.001 PHE H 140 TYR 0.016 0.001 TYR H 145 ARG 0.005 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 4.471 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.9107 (mtm) cc_final: 0.8888 (ttm) REVERT: B 321 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 368 MET cc_start: 0.3913 (tmm) cc_final: 0.3464 (mmp) REVERT: C 36 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.7673 (tmm) REVERT: C 95 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8983 (m-80) REVERT: D 56 MET cc_start: 0.8824 (mtp) cc_final: 0.8307 (mtt) REVERT: D 344 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7503 (ttp-170) REVERT: D 364 MET cc_start: 0.8050 (ttm) cc_final: 0.7754 (ttp) REVERT: E 95 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.6933 (m-10) REVERT: F 4 MET cc_start: 0.7760 (mmm) cc_final: 0.7243 (mmm) REVERT: F 66 ARG cc_start: 0.7830 (ptt-90) cc_final: 0.7474 (ptt-90) REVERT: F 84 GLU cc_start: 0.7426 (mp0) cc_final: 0.6794 (mp0) REVERT: F 168 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.7646 (m-90) REVERT: H 11 LEU cc_start: 0.8414 (tp) cc_final: 0.8053 (tt) REVERT: H 24 ARG cc_start: 0.7151 (mtp-110) cc_final: 0.6694 (ttm110) REVERT: H 87 ASP cc_start: 0.7956 (m-30) cc_final: 0.7690 (m-30) REVERT: H 149 ILE cc_start: 0.5919 (tt) cc_final: 0.5684 (tp) REVERT: I 155 GLU cc_start: 0.8923 (mp0) cc_final: 0.8692 (OUTLIER) REVERT: J 32 SER cc_start: 0.6990 (OUTLIER) cc_final: 0.6527 (p) REVERT: J 216 ARG cc_start: 0.6425 (ttp80) cc_final: 0.5910 (tpm170) outliers start: 35 outliers final: 21 residues processed: 267 average time/residue: 2.6583 time to fit residues: 837.9165 Evaluate side-chains 258 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 232 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 168 TRP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26029 Z= 0.259 Angle : 0.500 7.456 35502 Z= 0.256 Chirality : 0.043 0.213 4113 Planarity : 0.004 0.040 4389 Dihedral : 4.424 50.800 3722 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 15.81 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.34 (0.15), residues: 3127 helix: 2.27 (0.20), residues: 677 sheet: -0.19 (0.16), residues: 987 loop : -0.37 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 101 HIS 0.004 0.001 HIS A 305 PHE 0.010 0.001 PHE H 94 TYR 0.083 0.001 TYR F 191 ARG 0.003 0.000 ARG H 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 3.831 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.9141 (mtm) cc_final: 0.8905 (ttm) REVERT: B 321 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 368 MET cc_start: 0.4022 (tmm) cc_final: 0.3482 (mmp) REVERT: C 36 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.7744 (tmm) REVERT: C 95 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8979 (m-80) REVERT: D 56 MET cc_start: 0.8901 (mtp) cc_final: 0.8376 (mtt) REVERT: D 268 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: D 344 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.7550 (ttp-170) REVERT: D 364 MET cc_start: 0.8097 (ttm) cc_final: 0.7765 (ttp) REVERT: E 95 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.7008 (m-10) REVERT: F 4 MET cc_start: 0.7938 (mmm) cc_final: 0.7467 (mmm) REVERT: H 11 LEU cc_start: 0.8449 (tp) cc_final: 0.8075 (tt) REVERT: H 24 ARG cc_start: 0.7188 (mtp-110) cc_final: 0.6611 (ttm110) REVERT: H 87 ASP cc_start: 0.7970 (m-30) cc_final: 0.7674 (m-30) REVERT: H 149 ILE cc_start: 0.5903 (tt) cc_final: 0.5699 (tp) REVERT: H 180 MET cc_start: 0.6797 (tpp) cc_final: 0.6339 (tpt) REVERT: J 32 SER cc_start: 0.7042 (OUTLIER) cc_final: 0.6688 (p) REVERT: J 216 ARG cc_start: 0.6492 (ttp80) cc_final: 0.5984 (tpm170) outliers start: 38 outliers final: 22 residues processed: 265 average time/residue: 2.6440 time to fit residues: 839.0738 Evaluate side-chains 253 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 169 optimal weight: 0.6980 chunk 217 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26029 Z= 0.156 Angle : 0.475 7.771 35502 Z= 0.240 Chirality : 0.042 0.215 4113 Planarity : 0.004 0.041 4389 Dihedral : 4.282 50.922 3722 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 1.29 % Allowed : 16.16 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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 (0.15), residues: 3127 helix: 2.40 (0.20), residues: 675 sheet: -0.18 (0.16), residues: 990 loop : -0.30 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 101 HIS 0.003 0.000 HIS B 297 PHE 0.011 0.001 PHE I 173 TYR 0.025 0.001 TYR F 191 ARG 0.004 0.000 ARG F 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 4.454 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.9120 (mtm) cc_final: 0.8898 (ttm) REVERT: B 321 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8513 (mp) REVERT: B 368 MET cc_start: 0.3978 (tmm) cc_final: 0.3509 (mmp) REVERT: C 36 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.7706 (tmm) REVERT: C 95 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: D 56 MET cc_start: 0.8864 (mtp) cc_final: 0.8340 (mtt) REVERT: D 364 MET cc_start: 0.8077 (ttm) cc_final: 0.7745 (ttp) REVERT: E 95 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: F 4 MET cc_start: 0.7982 (mmm) cc_final: 0.7513 (mmm) REVERT: H 11 LEU cc_start: 0.8438 (tp) cc_final: 0.8083 (tt) REVERT: H 24 ARG cc_start: 0.7055 (mtp-110) cc_final: 0.6612 (ttm110) REVERT: H 87 ASP cc_start: 0.7989 (m-30) cc_final: 0.7687 (m-30) REVERT: J 32 SER cc_start: 0.7033 (OUTLIER) cc_final: 0.6747 (p) REVERT: J 216 ARG cc_start: 0.6476 (ttp80) cc_final: 0.5981 (tpm170) outliers start: 37 outliers final: 20 residues processed: 263 average time/residue: 2.4405 time to fit residues: 766.7409 Evaluate side-chains 252 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 202 optimal weight: 30.0000 chunk 146 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 233 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26029 Z= 0.174 Angle : 0.475 8.082 35502 Z= 0.241 Chirality : 0.042 0.184 4113 Planarity : 0.004 0.097 4389 Dihedral : 4.248 50.805 3722 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 1.11 % Allowed : 16.40 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.44 (0.15), residues: 3127 helix: 2.42 (0.20), residues: 675 sheet: -0.16 (0.16), residues: 1026 loop : -0.31 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 101 HIS 0.003 0.001 HIS B 297 PHE 0.011 0.001 PHE I 173 TYR 0.019 0.001 TYR F 191 ARG 0.004 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 238 time to evaluate : 4.073 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.9125 (mtm) cc_final: 0.8901 (ttm) REVERT: B 368 MET cc_start: 0.3983 (tmm) cc_final: 0.3516 (mmp) REVERT: C 36 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.7714 (tmm) REVERT: C 95 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8977 (m-80) REVERT: D 56 MET cc_start: 0.8866 (mtp) cc_final: 0.8337 (mtt) REVERT: D 364 MET cc_start: 0.8108 (ttm) cc_final: 0.7769 (ttp) REVERT: E 95 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: F 4 MET cc_start: 0.8024 (mmm) cc_final: 0.7397 (mmm) REVERT: F 84 GLU cc_start: 0.7160 (mp0) cc_final: 0.6375 (mp0) REVERT: F 168 TRP cc_start: 0.8819 (m-90) cc_final: 0.7941 (m-90) REVERT: F 180 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.6028 (tpt) REVERT: H 11 LEU cc_start: 0.8469 (tp) cc_final: 0.8098 (tt) REVERT: H 87 ASP cc_start: 0.7944 (m-30) cc_final: 0.7641 (m-30) REVERT: H 215 ASN cc_start: 0.7625 (p0) cc_final: 0.7393 (p0) REVERT: J 216 ARG cc_start: 0.6472 (ttp80) cc_final: 0.6006 (tpm170) outliers start: 32 outliers final: 22 residues processed: 264 average time/residue: 2.5083 time to fit residues: 797.5084 Evaluate side-chains 257 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 231 time to evaluate : 3.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.0170 chunk 284 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 276 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 275 optimal weight: 0.8980 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26029 Z= 0.264 Angle : 0.508 8.650 35502 Z= 0.258 Chirality : 0.043 0.192 4113 Planarity : 0.004 0.087 4389 Dihedral : 4.385 50.757 3722 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.51 % Rotamer: Outliers : 0.97 % Allowed : 16.64 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.35 (0.15), residues: 3127 helix: 2.31 (0.20), residues: 675 sheet: -0.18 (0.16), residues: 1023 loop : -0.39 (0.17), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 101 HIS 0.004 0.001 HIS A 305 PHE 0.012 0.001 PHE H 94 TYR 0.019 0.001 TYR H 145 ARG 0.004 0.000 ARG H 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 3.848 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: B 368 MET cc_start: 0.4285 (tmm) cc_final: 0.3667 (mmp) REVERT: C 36 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.7760 (tmm) REVERT: C 95 TYR cc_start: 0.9350 (OUTLIER) cc_final: 0.8973 (m-80) REVERT: D 56 MET cc_start: 0.8908 (mtp) cc_final: 0.8372 (mtt) REVERT: D 364 MET cc_start: 0.8146 (ttm) cc_final: 0.7776 (ttp) REVERT: E 95 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.7063 (m-10) REVERT: F 4 MET cc_start: 0.8109 (mmm) cc_final: 0.7486 (mmm) REVERT: F 180 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.6035 (tpt) REVERT: H 11 LEU cc_start: 0.8440 (tp) cc_final: 0.8088 (tt) REVERT: H 24 ARG cc_start: 0.7035 (mtp-110) cc_final: 0.6652 (ttm110) REVERT: H 87 ASP cc_start: 0.7967 (m-30) cc_final: 0.7666 (m-30) REVERT: H 215 ASN cc_start: 0.7636 (p0) cc_final: 0.7405 (p0) REVERT: J 216 ARG cc_start: 0.6507 (ttp80) cc_final: 0.6024 (tpm170) outliers start: 28 outliers final: 22 residues processed: 260 average time/residue: 2.5751 time to fit residues: 793.7520 Evaluate side-chains 256 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Chi-restraints excluded: chain K residue 195 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 5.9990 chunk 292 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 282 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26029 Z= 0.264 Angle : 0.513 11.079 35502 Z= 0.260 Chirality : 0.043 0.186 4113 Planarity : 0.004 0.081 4389 Dihedral : 4.434 50.868 3722 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.01 % Allowed : 16.82 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.32 (0.15), residues: 3127 helix: 2.24 (0.20), residues: 675 sheet: -0.13 (0.16), residues: 984 loop : -0.44 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.004 0.001 HIS B 297 PHE 0.014 0.001 PHE J 214 TYR 0.016 0.001 TYR H 145 ARG 0.009 0.000 ARG F 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6254 Ramachandran restraints generated. 3127 Oldfield, 0 Emsley, 3127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 4.145 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: B 368 MET cc_start: 0.4150 (tmm) cc_final: 0.3513 (mmp) REVERT: C 36 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.7742 (tmm) REVERT: C 95 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8967 (m-80) REVERT: D 56 MET cc_start: 0.8939 (mtp) cc_final: 0.8366 (mtt) REVERT: D 268 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: D 364 MET cc_start: 0.8183 (ttm) cc_final: 0.7771 (ttt) REVERT: E 95 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.7048 (m-10) REVERT: F 4 MET cc_start: 0.8189 (mmm) cc_final: 0.7543 (mmm) REVERT: F 72 SER cc_start: 0.7629 (t) cc_final: 0.7330 (p) REVERT: F 180 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.6037 (tpt) REVERT: G 158 THR cc_start: 0.9022 (m) cc_final: 0.8746 (p) REVERT: H 11 LEU cc_start: 0.8445 (tp) cc_final: 0.8071 (tt) REVERT: H 87 ASP cc_start: 0.8024 (m-30) cc_final: 0.7721 (m-30) REVERT: H 215 ASN cc_start: 0.7644 (p0) cc_final: 0.7423 (p0) REVERT: I 181 LEU cc_start: 0.9359 (mm) cc_final: 0.9086 (mm) REVERT: J 216 ARG cc_start: 0.6494 (ttp80) cc_final: 0.5920 (tpm170) outliers start: 29 outliers final: 20 residues processed: 261 average time/residue: 2.4936 time to fit residues: 790.2745 Evaluate side-chains 259 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 233 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 139 CYS Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090870 restraints weight = 93989.453| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.63 r_work: 0.2703 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26029 Z= 0.256 Angle : 0.511 10.299 35502 Z= 0.260 Chirality : 0.043 0.186 4113 Planarity : 0.004 0.078 4389 Dihedral : 4.439 50.878 3722 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 0.94 % Allowed : 16.96 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.99 % 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: 0.32 (0.15), residues: 3127 helix: 2.24 (0.20), residues: 675 sheet: -0.14 (0.16), residues: 984 loop : -0.44 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 101 HIS 0.004 0.001 HIS B 297 PHE 0.010 0.001 PHE C 254 TYR 0.015 0.001 TYR F 145 ARG 0.007 0.000 ARG F 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14932.87 seconds wall clock time: 264 minutes 9.08 seconds (15849.08 seconds total)