Starting phenix.real_space_refine on Mon Feb 19 23:54:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/02_2024/6o9z_0664_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/02_2024/6o9z_0664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/02_2024/6o9z_0664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/02_2024/6o9z_0664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/02_2024/6o9z_0664_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o9z_0664/02_2024/6o9z_0664_neut_updated.pdb" } resolution = 3.03 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= -0.011 sd= 0.787 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 124 5.16 5 C 16584 2.51 5 N 4335 2.21 5 O 4743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ASP 219": "OD1" <-> "OD2" Residue "C ASP 301": "OD1" <-> "OD2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ASP 459": "OD1" <-> "OD2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F ASP 459": "OD1" <-> "OD2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G ARG 74": "NH1" <-> "NH2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G ASP 248": "OD1" <-> "OD2" Residue "G GLU 299": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "H ASP 158": "OD1" <-> "OD2" Residue "H ASP 248": "OD1" <-> "OD2" Residue "H GLU 299": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "M ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25788 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3172 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 407} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3172 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 407} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 151 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2415 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 20, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2425 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 20, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2683 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 65 Chain: "F" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2683 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 65 Chain: "G" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2080 Classifications: {'peptide': 290} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "H" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2080 Classifications: {'peptide': 290} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 185 Chain: "J" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 185 Chain: "L" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 930 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 148} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 313 Chain: "M" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 930 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 148} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 313 Time building chain proxies: 12.59, per 1000 atoms: 0.49 Number of scatterers: 25788 At special positions: 0 Unit cell: (186.594, 171.798, 120.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 2 15.00 O 4743 8.00 N 4335 7.00 C 16584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.48 Conformation dependent library (CDL) restraints added in 5.2 seconds 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 44 sheets defined 37.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 303 through 314 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 31 through 46 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 97 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'C' and resid 147 through 157 removed outlier: 4.570A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 removed outlier: 4.455A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.886A pdb=" N ILE C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR C 337 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.737A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 127 through 144 Processing helix chain 'D' and resid 147 through 157 removed outlier: 4.535A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.162A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 219 through 225 removed outlier: 3.959A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'E' and resid 192 through 195 removed outlier: 3.897A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 195' Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 222 through 238 Processing helix chain 'E' and resid 248 through 266 removed outlier: 4.809A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 271 through 285 Processing helix chain 'E' and resid 293 through 311 Processing helix chain 'E' and resid 313 through 324 Processing helix chain 'E' and resid 340 through 352 Processing helix chain 'E' and resid 368 through 378 removed outlier: 4.036A pdb=" N HIS E 378 " --> pdb=" O SER E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 removed outlier: 3.925A pdb=" N SER E 392 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 429 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 460 through 462 No H-bonds generated for 'chain 'E' and resid 460 through 462' Processing helix chain 'E' and resid 512 through 517 Processing helix chain 'F' and resid 192 through 195 removed outlier: 3.897A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 192 through 195' Processing helix chain 'F' and resid 205 through 215 Processing helix chain 'F' and resid 222 through 238 Processing helix chain 'F' and resid 248 through 266 removed outlier: 4.809A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 271 through 285 Processing helix chain 'F' and resid 293 through 311 Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 340 through 352 Processing helix chain 'F' and resid 368 through 378 removed outlier: 4.037A pdb=" N HIS F 378 " --> pdb=" O SER F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 removed outlier: 3.925A pdb=" N SER F 392 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 429 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 512 through 517 Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 46 through 59 Processing helix chain 'G' and resid 63 through 76 Processing helix chain 'G' and resid 87 through 115 removed outlier: 4.011A pdb=" N ARG G 108 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 143 Processing helix chain 'G' and resid 161 through 169 Processing helix chain 'G' and resid 180 through 182 No H-bonds generated for 'chain 'G' and resid 180 through 182' Processing helix chain 'G' and resid 212 through 221 Processing helix chain 'G' and resid 248 through 251 No H-bonds generated for 'chain 'G' and resid 248 through 251' Processing helix chain 'G' and resid 278 through 280 No H-bonds generated for 'chain 'G' and resid 278 through 280' Processing helix chain 'G' and resid 293 through 304 Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 22 through 35 Processing helix chain 'H' and resid 46 through 59 Processing helix chain 'H' and resid 63 through 76 Processing helix chain 'H' and resid 87 through 115 removed outlier: 4.011A pdb=" N ARG H 108 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 143 Processing helix chain 'H' and resid 161 through 169 Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 212 through 221 Processing helix chain 'H' and resid 248 through 251 No H-bonds generated for 'chain 'H' and resid 248 through 251' Processing helix chain 'H' and resid 278 through 280 No H-bonds generated for 'chain 'H' and resid 278 through 280' Processing helix chain 'H' and resid 293 through 304 Processing helix chain 'I' and resid 35 through 45 Proline residue: I 39 - end of helix Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 86 through 92 Processing helix chain 'I' and resid 94 through 96 No H-bonds generated for 'chain 'I' and resid 94 through 96' Processing helix chain 'I' and resid 114 through 123 removed outlier: 3.639A pdb=" N VAL I 118 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA I 123 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 228 through 235 Processing helix chain 'I' and resid 283 through 291 removed outlier: 4.003A pdb=" N TRP I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 45 Proline residue: J 39 - end of helix Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'J' and resid 86 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 114 through 123 removed outlier: 3.638A pdb=" N VAL J 118 " --> pdb=" O HIS J 115 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA J 123 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 228 through 235 Processing helix chain 'J' and resid 283 through 291 removed outlier: 4.003A pdb=" N TRP J 290 " --> pdb=" O ARG J 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 38 No H-bonds generated for 'chain 'L' and resid 36 through 38' Processing helix chain 'L' and resid 91 through 117 Processing helix chain 'L' and resid 123 through 141 Processing helix chain 'L' and resid 146 through 157 removed outlier: 3.688A pdb=" N SER L 157 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 162 Processing helix chain 'L' and resid 169 through 179 Processing helix chain 'M' and resid 36 through 38 No H-bonds generated for 'chain 'M' and resid 36 through 38' Processing helix chain 'M' and resid 91 through 117 Processing helix chain 'M' and resid 123 through 141 Processing helix chain 'M' and resid 146 through 157 removed outlier: 3.687A pdb=" N SER M 157 " --> pdb=" O LYS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 162 Processing helix chain 'M' and resid 169 through 179 Processing sheet with id= A, first strand: chain 'A' and resid 149 through 152 removed outlier: 6.628A pdb=" N GLU A 90 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU A 47 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE A 92 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 155 through 157 Processing sheet with id= C, first strand: chain 'A' and resid 288 through 292 Processing sheet with id= D, first strand: chain 'A' and resid 239 through 241 removed outlier: 6.230A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= F, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.640A pdb=" N SER A 377 " --> pdb=" O LEU A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 373 through 375 Processing sheet with id= H, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.727A pdb=" N SER A 429 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 447 " --> pdb=" O VAL A 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.628A pdb=" N GLU B 90 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 47 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE B 92 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 155 through 157 Processing sheet with id= K, first strand: chain 'B' and resid 288 through 292 Processing sheet with id= L, first strand: chain 'B' and resid 239 through 241 removed outlier: 6.230A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 335 through 337 Processing sheet with id= N, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.640A pdb=" N SER B 377 " --> pdb=" O LEU B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 373 through 375 Processing sheet with id= P, first strand: chain 'B' and resid 411 through 413 removed outlier: 6.727A pdb=" N SER B 429 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER B 447 " --> pdb=" O VAL B 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.320A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 217 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 232 through 234 removed outlier: 7.095A pdb=" N LEU C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 245 through 248 Processing sheet with id= T, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.313A pdb=" N HIS D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR D 167 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE D 190 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 217 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 232 through 234 removed outlier: 7.185A pdb=" N LEU D 323 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 245 through 248 Processing sheet with id= W, first strand: chain 'E' and resid 332 through 336 removed outlier: 6.626A pdb=" N ARG E 357 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL E 335 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 359 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL E 360 " --> pdb=" O PRO E 382 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER E 384 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP E 362 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU E 386 " --> pdb=" O ASP E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 400 through 404 removed outlier: 8.006A pdb=" N LEU E 403 " --> pdb=" O PRO E 433 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU E 435 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU E 499 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 414 through 417 Processing sheet with id= Z, first strand: chain 'F' and resid 332 through 336 removed outlier: 6.626A pdb=" N ARG F 357 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL F 335 " --> pdb=" O ARG F 357 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL F 359 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL F 360 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER F 384 " --> pdb=" O VAL F 360 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP F 362 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU F 386 " --> pdb=" O ASP F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 400 through 404 removed outlier: 8.006A pdb=" N LEU F 403 " --> pdb=" O PRO F 433 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU F 435 " --> pdb=" O LEU F 403 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU F 499 " --> pdb=" O VAL F 436 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 414 through 417 Processing sheet with id= AC, first strand: chain 'G' and resid 123 through 127 removed outlier: 7.518A pdb=" N VAL G 152 " --> pdb=" O PRO G 174 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR G 176 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 192 through 196 removed outlier: 7.593A pdb=" N VAL G 195 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR G 227 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU G 283 " --> pdb=" O VAL G 228 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 206 through 208 Processing sheet with id= AF, first strand: chain 'H' and resid 123 through 127 removed outlier: 7.518A pdb=" N VAL H 152 " --> pdb=" O PRO H 174 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR H 176 " --> pdb=" O VAL H 152 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 192 through 196 removed outlier: 7.594A pdb=" N VAL H 195 " --> pdb=" O PRO H 225 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR H 227 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU H 283 " --> pdb=" O VAL H 228 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 206 through 208 Processing sheet with id= AI, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.646A pdb=" N ASP I 100 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL I 6 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU I 102 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET I 8 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU I 104 " --> pdb=" O MET I 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'I' and resid 51 through 54 Processing sheet with id= AK, first strand: chain 'I' and resid 128 through 133 Processing sheet with id= AL, first strand: chain 'I' and resid 193 through 196 removed outlier: 5.754A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 3 through 8 removed outlier: 6.646A pdb=" N ASP J 100 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL J 6 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU J 102 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET J 8 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU J 104 " --> pdb=" O MET J 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'J' and resid 51 through 54 Processing sheet with id= AO, first strand: chain 'J' and resid 128 through 133 Processing sheet with id= AP, first strand: chain 'J' and resid 193 through 196 removed outlier: 5.754A pdb=" N ASP J 161 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU J 167 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'L' and resid 67 through 71 removed outlier: 6.912A pdb=" N TYR L 32 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE L 26 " --> pdb=" O GLY L 30 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE L 82 " --> pdb=" O MET L 44 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU L 46 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU L 84 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER L 85 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL L 72 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 67 through 71 removed outlier: 6.913A pdb=" N TYR M 32 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE M 26 " --> pdb=" O GLY M 30 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY M 30 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE M 82 " --> pdb=" O MET M 44 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU M 46 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU M 84 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER M 85 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL M 72 " --> pdb=" O SER M 85 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2820 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: 8.82 Time building geometry restraints manager: 11.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8528 1.34 - 1.46: 4992 1.46 - 1.58: 12495 1.58 - 1.70: 8 1.70 - 1.81: 190 Bond restraints: 26213 Sorted by residual: bond pdb=" CD2 TRP A 97 " pdb=" CE2 TRP A 97 " ideal model delta sigma weight residual 1.409 1.445 -0.036 1.70e-02 3.46e+03 4.37e+00 bond pdb=" CD2 TRP C 51 " pdb=" CE2 TRP C 51 " ideal model delta sigma weight residual 1.409 1.444 -0.035 1.70e-02 3.46e+03 4.32e+00 bond pdb=" CD2 TRP B 97 " pdb=" CE2 TRP B 97 " ideal model delta sigma weight residual 1.409 1.444 -0.035 1.70e-02 3.46e+03 4.21e+00 bond pdb=" CD2 TRP D 51 " pdb=" CE2 TRP D 51 " ideal model delta sigma weight residual 1.409 1.443 -0.034 1.70e-02 3.46e+03 4.01e+00 bond pdb=" CD2 TRP F 476 " pdb=" CE2 TRP F 476 " ideal model delta sigma weight residual 1.409 1.441 -0.032 1.70e-02 3.46e+03 3.52e+00 ... (remaining 26208 not shown) Histogram of bond angle deviations from ideal: 97.68 - 104.90: 472 104.90 - 112.11: 13799 112.11 - 119.33: 8538 119.33 - 126.54: 12519 126.54 - 133.76: 271 Bond angle restraints: 35599 Sorted by residual: angle pdb=" N GLN G 156 " pdb=" CA GLN G 156 " pdb=" C GLN G 156 " ideal model delta sigma weight residual 109.81 119.94 -10.13 2.21e+00 2.05e-01 2.10e+01 angle pdb=" N GLN H 156 " pdb=" CA GLN H 156 " pdb=" C GLN H 156 " ideal model delta sigma weight residual 109.81 119.94 -10.13 2.21e+00 2.05e-01 2.10e+01 angle pdb=" N ALA G 295 " pdb=" CA ALA G 295 " pdb=" C ALA G 295 " ideal model delta sigma weight residual 113.23 107.63 5.60 1.24e+00 6.50e-01 2.04e+01 angle pdb=" N ALA H 295 " pdb=" CA ALA H 295 " pdb=" C ALA H 295 " ideal model delta sigma weight residual 113.23 107.65 5.58 1.24e+00 6.50e-01 2.03e+01 angle pdb=" N CYS H 57 " pdb=" CA CYS H 57 " pdb=" C CYS H 57 " ideal model delta sigma weight residual 113.41 108.22 5.19 1.22e+00 6.72e-01 1.81e+01 ... (remaining 35594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 14776 17.32 - 34.65: 831 34.65 - 51.97: 147 51.97 - 69.30: 38 69.30 - 86.62: 27 Dihedral angle restraints: 15819 sinusoidal: 5384 harmonic: 10435 Sorted by residual: dihedral pdb=" CA ASN D 242 " pdb=" C ASN D 242 " pdb=" N GLY D 243 " pdb=" CA GLY D 243 " ideal model delta harmonic sigma weight residual 180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LYS G 209 " pdb=" C LYS G 209 " pdb=" N ILE G 210 " pdb=" CA ILE G 210 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LYS H 209 " pdb=" C LYS H 209 " pdb=" N ILE H 210 " pdb=" CA ILE H 210 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 15816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3329 0.060 - 0.119: 938 0.119 - 0.179: 103 0.179 - 0.238: 15 0.238 - 0.298: 2 Chirality restraints: 4387 Sorted by residual: chirality pdb=" CB VAL G 236 " pdb=" CA VAL G 236 " pdb=" CG1 VAL G 236 " pdb=" CG2 VAL G 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB VAL H 236 " pdb=" CA VAL H 236 " pdb=" CG1 VAL H 236 " pdb=" CG2 VAL H 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA MET H 1 " pdb=" N MET H 1 " pdb=" C MET H 1 " pdb=" CB MET H 1 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4384 not shown) Planarity restraints: 4526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 294 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.69e+01 pdb=" C SER H 294 " 0.071 2.00e-02 2.50e+03 pdb=" O SER H 294 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA H 295 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 294 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C SER G 294 " 0.071 2.00e-02 2.50e+03 pdb=" O SER G 294 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA G 295 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 368 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU E 368 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU E 368 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY E 369 " 0.019 2.00e-02 2.50e+03 ... (remaining 4523 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3111 2.73 - 3.28: 25441 3.28 - 3.82: 42610 3.82 - 4.36: 49676 4.36 - 4.90: 86113 Nonbonded interactions: 206951 Sorted by model distance: nonbonded pdb=" OE1 GLU D 193 " pdb=" NE2 HIS D 201 " model vdw 2.192 2.520 nonbonded pdb=" OG1 THR F 440 " pdb=" OE2 GLU F 503 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR E 440 " pdb=" OE2 GLU E 503 " model vdw 2.236 2.440 nonbonded pdb=" NE2 GLN H 243 " pdb=" O TYR H 275 " model vdw 2.238 2.520 nonbonded pdb=" NE2 GLN G 243 " pdb=" O TYR G 275 " model vdw 2.239 2.520 ... (remaining 206946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.120 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 70.340 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.008 0.071 26213 Z= 0.523 Angle : 0.929 11.048 35599 Z= 0.522 Chirality : 0.054 0.298 4387 Planarity : 0.007 0.057 4526 Dihedral : 12.406 86.619 8969 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.48 % Allowed : 5.13 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.12), residues: 3555 helix: -1.78 (0.11), residues: 1387 sheet: -2.11 (0.22), residues: 471 loop : -2.10 (0.13), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 37 HIS 0.011 0.002 HIS B 105 PHE 0.036 0.003 PHE H 239 TYR 0.022 0.002 TYR D 335 ARG 0.003 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 763 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7510 (t0) cc_final: 0.7110 (t0) REVERT: A 276 LEU cc_start: 0.8888 (tp) cc_final: 0.8677 (tp) REVERT: A 312 ASP cc_start: 0.7983 (m-30) cc_final: 0.7702 (m-30) REVERT: B 50 ASP cc_start: 0.7656 (t0) cc_final: 0.7269 (t0) REVERT: C 20 GLU cc_start: 0.8684 (tt0) cc_final: 0.7676 (tm-30) REVERT: C 44 GLN cc_start: 0.8018 (tt0) cc_final: 0.7745 (tt0) REVERT: C 48 ASP cc_start: 0.8029 (m-30) cc_final: 0.7755 (m-30) REVERT: C 68 MET cc_start: 0.8423 (mtp) cc_final: 0.7707 (ttp) REVERT: C 96 LEU cc_start: 0.7568 (mt) cc_final: 0.7359 (tt) REVERT: C 163 GLU cc_start: 0.7479 (tt0) cc_final: 0.7176 (tt0) REVERT: C 209 LYS cc_start: 0.9138 (mttt) cc_final: 0.8911 (mtmt) REVERT: C 237 LYS cc_start: 0.8490 (tptt) cc_final: 0.8242 (tptp) REVERT: D 44 GLN cc_start: 0.8007 (tt0) cc_final: 0.7766 (tt0) REVERT: D 242 ASN cc_start: 0.8588 (m110) cc_final: 0.8235 (m-40) REVERT: E 236 VAL cc_start: 0.9101 (t) cc_final: 0.8847 (t) REVERT: E 362 ASP cc_start: 0.8445 (t0) cc_final: 0.8239 (t0) REVERT: E 439 GLU cc_start: 0.8692 (mp0) cc_final: 0.8115 (mp0) REVERT: E 462 ASP cc_start: 0.8437 (m-30) cc_final: 0.8205 (m-30) REVERT: F 236 VAL cc_start: 0.9100 (t) cc_final: 0.8850 (t) REVERT: F 362 ASP cc_start: 0.8436 (t0) cc_final: 0.8184 (t70) REVERT: F 367 LEU cc_start: 0.9186 (mt) cc_final: 0.8975 (mm) REVERT: F 439 GLU cc_start: 0.8701 (mp0) cc_final: 0.8125 (mp0) REVERT: F 462 ASP cc_start: 0.8433 (m-30) cc_final: 0.8190 (m-30) REVERT: G 17 ASP cc_start: 0.8305 (t0) cc_final: 0.8046 (t0) REVERT: G 75 PHE cc_start: 0.8835 (t80) cc_final: 0.8291 (t80) REVERT: G 187 MET cc_start: 0.8889 (tpp) cc_final: 0.8604 (tpt) REVERT: G 244 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8287 (tp40) REVERT: G 245 ASP cc_start: 0.8804 (t0) cc_final: 0.8455 (t0) REVERT: G 290 VAL cc_start: 0.9384 (t) cc_final: 0.9074 (t) REVERT: H 17 ASP cc_start: 0.8312 (t0) cc_final: 0.8079 (t0) REVERT: H 75 PHE cc_start: 0.8861 (t80) cc_final: 0.8281 (t80) REVERT: H 187 MET cc_start: 0.8886 (tpp) cc_final: 0.8471 (tpt) REVERT: H 244 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8274 (tp40) REVERT: H 245 ASP cc_start: 0.8854 (t0) cc_final: 0.8521 (t0) REVERT: H 290 VAL cc_start: 0.9357 (t) cc_final: 0.8953 (t) REVERT: I 125 ASP cc_start: 0.8826 (t70) cc_final: 0.8527 (t0) REVERT: I 161 ASP cc_start: 0.7032 (t70) cc_final: 0.6816 (p0) REVERT: J 125 ASP cc_start: 0.8774 (t70) cc_final: 0.8484 (t0) outliers start: 12 outliers final: 2 residues processed: 769 average time/residue: 0.3592 time to fit residues: 448.5198 Evaluate side-chains 554 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 552 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 76 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.9980 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 279 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 323 optimal weight: 50.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 352 HIS B 393 GLN C 188 HIS C 261 HIS D 132 ASN D 242 ASN D 261 HIS ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN E 274 HIS E 281 ASN E 422 GLN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 HIS F 281 ASN ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS H 128 HIS H 156 GLN I 115 HIS I 188 GLN J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26213 Z= 0.260 Angle : 0.595 9.130 35599 Z= 0.328 Chirality : 0.045 0.174 4387 Planarity : 0.004 0.055 4526 Dihedral : 4.553 32.215 3615 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.26 % Allowed : 14.23 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 3555 helix: -0.04 (0.13), residues: 1390 sheet: -1.67 (0.22), residues: 489 loop : -1.39 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 37 HIS 0.007 0.001 HIS I 115 PHE 0.023 0.002 PHE D 278 TYR 0.013 0.001 TYR C 337 ARG 0.004 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 602 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7459 (t0) cc_final: 0.7110 (t0) REVERT: A 324 GLU cc_start: 0.8911 (pm20) cc_final: 0.8695 (pm20) REVERT: B 50 ASP cc_start: 0.7501 (t0) cc_final: 0.7178 (t0) REVERT: B 324 GLU cc_start: 0.8922 (pm20) cc_final: 0.8712 (pm20) REVERT: C 44 GLN cc_start: 0.7903 (tt0) cc_final: 0.7693 (tt0) REVERT: C 48 ASP cc_start: 0.8141 (m-30) cc_final: 0.7871 (m-30) REVERT: C 68 MET cc_start: 0.8412 (mtp) cc_final: 0.8155 (mtm) REVERT: D 16 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8433 (mm-30) REVERT: D 217 MET cc_start: 0.8205 (ptt) cc_final: 0.7880 (ptt) REVERT: E 439 GLU cc_start: 0.8596 (mp0) cc_final: 0.7946 (mp0) REVERT: E 461 ASP cc_start: 0.8201 (t0) cc_final: 0.7896 (m-30) REVERT: F 439 GLU cc_start: 0.8606 (mp0) cc_final: 0.7954 (mp0) REVERT: F 461 ASP cc_start: 0.8206 (t0) cc_final: 0.7899 (m-30) REVERT: G 17 ASP cc_start: 0.8379 (t0) cc_final: 0.8155 (t0) REVERT: G 75 PHE cc_start: 0.8830 (t80) cc_final: 0.8258 (t80) REVERT: G 244 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8184 (tp40) REVERT: H 75 PHE cc_start: 0.8856 (t80) cc_final: 0.8225 (t80) REVERT: H 244 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8184 (tp40) REVERT: H 290 VAL cc_start: 0.9273 (t) cc_final: 0.9032 (t) REVERT: I 125 ASP cc_start: 0.8741 (t70) cc_final: 0.8495 (t0) REVERT: I 161 ASP cc_start: 0.7231 (t70) cc_final: 0.6869 (p0) REVERT: J 2 GLU cc_start: 0.5207 (tt0) cc_final: 0.4915 (tt0) REVERT: J 125 ASP cc_start: 0.8706 (t70) cc_final: 0.8445 (t0) REVERT: J 161 ASP cc_start: 0.7410 (t70) cc_final: 0.6984 (p0) outliers start: 82 outliers final: 58 residues processed: 639 average time/residue: 0.3298 time to fit residues: 347.9064 Evaluate side-chains 601 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 543 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 323 optimal weight: 50.0000 chunk 349 optimal weight: 20.0000 chunk 288 optimal weight: 1.9990 chunk 321 optimal weight: 50.0000 chunk 110 optimal weight: 6.9990 chunk 259 optimal weight: 0.0870 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 352 HIS ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 128 GLN D 132 ASN D 331 ASN E 265 GLN E 431 ASN F 213 GLN F 245 ASN F 265 GLN F 431 ASN G 270 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26213 Z= 0.230 Angle : 0.559 8.681 35599 Z= 0.307 Chirality : 0.044 0.175 4387 Planarity : 0.004 0.054 4526 Dihedral : 4.266 30.945 3615 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.02 % Allowed : 16.38 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.58 (0.14), residues: 3555 helix: 0.80 (0.14), residues: 1390 sheet: -1.46 (0.22), residues: 539 loop : -0.98 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 37 HIS 0.006 0.001 HIS H 128 PHE 0.018 0.001 PHE D 177 TYR 0.013 0.001 TYR C 337 ARG 0.002 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 592 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7419 (t0) cc_final: 0.7073 (t0) REVERT: A 324 GLU cc_start: 0.8942 (pm20) cc_final: 0.8690 (pm20) REVERT: A 423 VAL cc_start: 0.8883 (t) cc_final: 0.8667 (t) REVERT: B 50 ASP cc_start: 0.7503 (t0) cc_final: 0.7165 (t0) REVERT: B 324 GLU cc_start: 0.8946 (pm20) cc_final: 0.8718 (pm20) REVERT: C 32 GLU cc_start: 0.8646 (tt0) cc_final: 0.7923 (tm-30) REVERT: C 44 GLN cc_start: 0.7981 (tt0) cc_final: 0.7777 (tt0) REVERT: C 48 ASP cc_start: 0.8179 (m-30) cc_final: 0.7936 (m-30) REVERT: C 68 MET cc_start: 0.8487 (mtp) cc_final: 0.8255 (mtm) REVERT: C 303 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8843 (mp) REVERT: D 32 GLU cc_start: 0.8820 (tt0) cc_final: 0.8261 (tm-30) REVERT: D 217 MET cc_start: 0.8184 (ptt) cc_final: 0.7830 (ptt) REVERT: D 278 PHE cc_start: 0.7429 (m-80) cc_final: 0.7208 (m-80) REVERT: E 207 MET cc_start: 0.8522 (mmm) cc_final: 0.8033 (mmm) REVERT: E 310 GLU cc_start: 0.8130 (pt0) cc_final: 0.7908 (pt0) REVERT: E 439 GLU cc_start: 0.8589 (mp0) cc_final: 0.7938 (mp0) REVERT: F 207 MET cc_start: 0.8526 (mmm) cc_final: 0.8031 (mmm) REVERT: F 310 GLU cc_start: 0.8142 (pt0) cc_final: 0.7921 (pt0) REVERT: F 439 GLU cc_start: 0.8576 (mp0) cc_final: 0.7924 (mp0) REVERT: G 17 ASP cc_start: 0.8405 (t0) cc_final: 0.8204 (t0) REVERT: G 75 PHE cc_start: 0.8855 (t80) cc_final: 0.8287 (t80) REVERT: G 164 MET cc_start: 0.8490 (ttt) cc_final: 0.7830 (tpp) REVERT: G 244 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8175 (tp40) REVERT: H 75 PHE cc_start: 0.8852 (t80) cc_final: 0.8284 (t80) REVERT: H 164 MET cc_start: 0.8521 (ttt) cc_final: 0.7851 (tpp) REVERT: H 244 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8109 (tp40) REVERT: H 290 VAL cc_start: 0.9270 (t) cc_final: 0.9045 (t) REVERT: I 125 ASP cc_start: 0.8719 (t70) cc_final: 0.8478 (t0) REVERT: I 161 ASP cc_start: 0.7306 (t70) cc_final: 0.6941 (p0) REVERT: J 125 ASP cc_start: 0.8779 (t70) cc_final: 0.8509 (t0) REVERT: J 161 ASP cc_start: 0.7517 (t70) cc_final: 0.7122 (p0) outliers start: 101 outliers final: 76 residues processed: 641 average time/residue: 0.3076 time to fit residues: 329.0624 Evaluate side-chains 634 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 557 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 206 CYS Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 263 ILE Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 9.9990 chunk 243 optimal weight: 0.0970 chunk 168 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 325 optimal weight: 30.0000 chunk 344 optimal weight: 0.4980 chunk 169 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 352 HIS ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN E 431 ASN F 216 GLN F 431 ASN H 128 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26213 Z= 0.206 Angle : 0.537 8.844 35599 Z= 0.295 Chirality : 0.043 0.155 4387 Planarity : 0.004 0.053 4526 Dihedral : 4.148 32.012 3615 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.82 % Allowed : 18.85 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.16 (0.14), residues: 3555 helix: 1.16 (0.14), residues: 1390 sheet: -1.09 (0.23), residues: 509 loop : -0.83 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 37 HIS 0.005 0.001 HIS C 160 PHE 0.018 0.001 PHE C 278 TYR 0.012 0.001 TYR C 337 ARG 0.001 0.000 ARG G 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 582 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7400 (t0) cc_final: 0.7043 (t0) REVERT: A 107 LEU cc_start: 0.8522 (tp) cc_final: 0.8211 (mp) REVERT: A 324 GLU cc_start: 0.8933 (pm20) cc_final: 0.8593 (pm20) REVERT: A 418 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: A 423 VAL cc_start: 0.8896 (t) cc_final: 0.8673 (t) REVERT: B 50 ASP cc_start: 0.7462 (t0) cc_final: 0.7096 (t0) REVERT: B 305 MET cc_start: 0.8610 (mmm) cc_final: 0.8166 (tpt) REVERT: B 324 GLU cc_start: 0.8936 (pm20) cc_final: 0.8600 (pm20) REVERT: C 32 GLU cc_start: 0.8667 (tt0) cc_final: 0.7919 (tm-30) REVERT: C 48 ASP cc_start: 0.8187 (m-30) cc_final: 0.7967 (m-30) REVERT: C 64 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7202 (tm-30) REVERT: C 303 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8841 (mp) REVERT: D 217 MET cc_start: 0.8080 (ptt) cc_final: 0.7747 (ptt) REVERT: D 303 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8802 (mp) REVERT: E 207 MET cc_start: 0.8522 (mmm) cc_final: 0.8023 (mmm) REVERT: E 310 GLU cc_start: 0.8162 (pt0) cc_final: 0.7946 (pt0) REVERT: E 362 ASP cc_start: 0.8384 (t0) cc_final: 0.8124 (t70) REVERT: E 439 GLU cc_start: 0.8566 (mp0) cc_final: 0.7861 (mp0) REVERT: E 462 ASP cc_start: 0.8556 (m-30) cc_final: 0.8187 (m-30) REVERT: E 506 MET cc_start: 0.8089 (mtm) cc_final: 0.7875 (mtm) REVERT: F 207 MET cc_start: 0.8532 (mmm) cc_final: 0.8055 (mmm) REVERT: F 310 GLU cc_start: 0.8175 (pt0) cc_final: 0.7957 (pt0) REVERT: F 362 ASP cc_start: 0.8374 (t0) cc_final: 0.8109 (t70) REVERT: F 431 ASN cc_start: 0.8076 (p0) cc_final: 0.7869 (p0) REVERT: F 439 GLU cc_start: 0.8571 (mp0) cc_final: 0.7886 (mp0) REVERT: F 462 ASP cc_start: 0.8572 (m-30) cc_final: 0.8154 (m-30) REVERT: F 506 MET cc_start: 0.8096 (mtm) cc_final: 0.7886 (mtm) REVERT: G 75 PHE cc_start: 0.8865 (t80) cc_final: 0.8298 (t80) REVERT: G 164 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7852 (tpp) REVERT: G 187 MET cc_start: 0.8830 (tpt) cc_final: 0.8575 (tpt) REVERT: G 244 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8184 (tp40) REVERT: H 75 PHE cc_start: 0.8843 (t80) cc_final: 0.8272 (t80) REVERT: H 244 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8110 (tp40) REVERT: H 290 VAL cc_start: 0.9259 (t) cc_final: 0.9023 (t) REVERT: I 125 ASP cc_start: 0.8765 (t70) cc_final: 0.8519 (t0) REVERT: I 161 ASP cc_start: 0.7318 (t70) cc_final: 0.6935 (p0) REVERT: I 209 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8394 (mmtt) REVERT: J 125 ASP cc_start: 0.8796 (t70) cc_final: 0.8536 (t0) REVERT: J 161 ASP cc_start: 0.7495 (t70) cc_final: 0.7098 (p0) REVERT: J 209 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8356 (mmtt) outliers start: 96 outliers final: 78 residues processed: 623 average time/residue: 0.3161 time to fit residues: 327.9740 Evaluate side-chains 636 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 554 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 206 CYS Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 263 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 20.0000 chunk 237 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 HIS C 44 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN L 67 ASN M 67 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26213 Z= 0.296 Angle : 0.582 8.594 35599 Z= 0.318 Chirality : 0.044 0.162 4387 Planarity : 0.004 0.053 4526 Dihedral : 4.326 32.063 3615 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.93 % Allowed : 19.32 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.01 (0.14), residues: 3555 helix: 1.29 (0.14), residues: 1388 sheet: -1.02 (0.23), residues: 509 loop : -0.74 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 37 HIS 0.006 0.001 HIS C 160 PHE 0.019 0.002 PHE D 177 TYR 0.013 0.001 TYR A 128 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 560 time to evaluate : 3.412 Fit side-chains REVERT: A 50 ASP cc_start: 0.7452 (t0) cc_final: 0.7148 (t0) REVERT: A 107 LEU cc_start: 0.8606 (tp) cc_final: 0.8333 (mp) REVERT: A 324 GLU cc_start: 0.8954 (pm20) cc_final: 0.8551 (pm20) REVERT: B 50 ASP cc_start: 0.7491 (t0) cc_final: 0.7198 (t0) REVERT: B 324 GLU cc_start: 0.8942 (pm20) cc_final: 0.8540 (pm20) REVERT: C 292 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7743 (tm-30) REVERT: C 303 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8901 (mp) REVERT: D 303 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8865 (mp) REVERT: E 310 GLU cc_start: 0.8289 (pt0) cc_final: 0.8068 (pt0) REVERT: E 439 GLU cc_start: 0.8631 (mp0) cc_final: 0.7950 (mp0) REVERT: E 506 MET cc_start: 0.8157 (mtm) cc_final: 0.7925 (mtm) REVERT: F 310 GLU cc_start: 0.8299 (pt0) cc_final: 0.8076 (pt0) REVERT: F 362 ASP cc_start: 0.8426 (t0) cc_final: 0.8162 (t70) REVERT: F 439 GLU cc_start: 0.8640 (mp0) cc_final: 0.7975 (mp0) REVERT: F 506 MET cc_start: 0.8159 (mtm) cc_final: 0.7922 (mtm) REVERT: G 17 ASP cc_start: 0.8239 (t0) cc_final: 0.7897 (t0) REVERT: G 75 PHE cc_start: 0.8892 (t80) cc_final: 0.8351 (t80) REVERT: G 164 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7822 (ttt) REVERT: G 244 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8285 (tp40) REVERT: H 17 ASP cc_start: 0.8238 (t0) cc_final: 0.7936 (t0) REVERT: H 75 PHE cc_start: 0.8893 (t80) cc_final: 0.8308 (t80) REVERT: H 164 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7809 (ttt) REVERT: H 242 ASN cc_start: 0.8560 (p0) cc_final: 0.8286 (p0) REVERT: H 244 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8390 (tp40) REVERT: H 290 VAL cc_start: 0.9339 (t) cc_final: 0.9131 (t) REVERT: I 125 ASP cc_start: 0.8827 (t70) cc_final: 0.8620 (t0) REVERT: I 209 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8418 (mmtt) REVERT: J 50 GLU cc_start: 0.7765 (tt0) cc_final: 0.7327 (mp0) REVERT: J 125 ASP cc_start: 0.8868 (t70) cc_final: 0.8622 (t0) REVERT: J 161 ASP cc_start: 0.7573 (t70) cc_final: 0.7191 (p0) outliers start: 124 outliers final: 98 residues processed: 618 average time/residue: 0.3161 time to fit residues: 326.9298 Evaluate side-chains 650 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 548 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 206 CYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 10.0000 chunk 309 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 344 optimal weight: 30.0000 chunk 285 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS I 115 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26213 Z= 0.277 Angle : 0.570 8.132 35599 Z= 0.313 Chirality : 0.044 0.189 4387 Planarity : 0.004 0.053 4526 Dihedral : 4.336 31.888 3615 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.13 % Allowed : 19.60 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.11 (0.15), residues: 3555 helix: 1.39 (0.14), residues: 1388 sheet: -0.98 (0.23), residues: 509 loop : -0.67 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 37 HIS 0.007 0.001 HIS J 115 PHE 0.020 0.001 PHE C 177 TYR 0.014 0.001 TYR A 128 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 557 time to evaluate : 2.756 Fit side-chains REVERT: A 50 ASP cc_start: 0.7436 (t0) cc_final: 0.7150 (t0) REVERT: A 106 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8168 (tt) REVERT: A 418 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: B 50 ASP cc_start: 0.7465 (t0) cc_final: 0.7167 (t0) REVERT: C 292 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 303 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8883 (mp) REVERT: D 20 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8522 (tp30) REVERT: D 303 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8875 (mp) REVERT: E 310 GLU cc_start: 0.8278 (pt0) cc_final: 0.8059 (pt0) REVERT: E 362 ASP cc_start: 0.8436 (t0) cc_final: 0.8168 (t70) REVERT: E 439 GLU cc_start: 0.8642 (mp0) cc_final: 0.8071 (mp0) REVERT: F 239 ASP cc_start: 0.8103 (t0) cc_final: 0.7799 (t0) REVERT: F 310 GLU cc_start: 0.8299 (pt0) cc_final: 0.8082 (pt0) REVERT: F 362 ASP cc_start: 0.8434 (t0) cc_final: 0.8181 (t70) REVERT: F 439 GLU cc_start: 0.8643 (mp0) cc_final: 0.8071 (mp0) REVERT: F 462 ASP cc_start: 0.8657 (m-30) cc_final: 0.8342 (m-30) REVERT: G 75 PHE cc_start: 0.8898 (t80) cc_final: 0.8346 (t80) REVERT: G 164 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7805 (ttt) REVERT: G 187 MET cc_start: 0.8926 (tpt) cc_final: 0.8584 (tpt) REVERT: G 244 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8326 (tp40) REVERT: H 17 ASP cc_start: 0.8312 (t0) cc_final: 0.7974 (t0) REVERT: H 75 PHE cc_start: 0.8907 (t80) cc_final: 0.8311 (t80) REVERT: H 113 ASP cc_start: 0.7960 (m-30) cc_final: 0.7691 (m-30) REVERT: H 164 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7738 (tpp) REVERT: H 244 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8276 (tp40) REVERT: H 290 VAL cc_start: 0.9343 (t) cc_final: 0.9142 (t) REVERT: I 125 ASP cc_start: 0.8815 (t70) cc_final: 0.8605 (t0) REVERT: I 206 CYS cc_start: 0.7097 (m) cc_final: 0.6680 (m) REVERT: I 209 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8127 (mmmt) REVERT: J 1 MET cc_start: 0.6345 (tpt) cc_final: 0.6092 (tpt) REVERT: J 125 ASP cc_start: 0.8859 (t70) cc_final: 0.8633 (t0) outliers start: 129 outliers final: 101 residues processed: 614 average time/residue: 0.2684 time to fit residues: 274.7808 Evaluate side-chains 645 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 538 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 196 MET Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 6.9990 chunk 38 optimal weight: 0.0670 chunk 196 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 289 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 214 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN E 470 HIS I 115 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26213 Z= 0.194 Angle : 0.534 7.790 35599 Z= 0.295 Chirality : 0.043 0.171 4387 Planarity : 0.004 0.052 4526 Dihedral : 4.101 31.624 3615 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.57 % Allowed : 21.59 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 3555 helix: 1.63 (0.14), residues: 1385 sheet: -0.91 (0.23), residues: 522 loop : -0.53 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 37 HIS 0.007 0.001 HIS J 115 PHE 0.019 0.001 PHE D 177 TYR 0.011 0.001 TYR G 304 ARG 0.001 0.000 ARG F 517 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 576 time to evaluate : 3.138 Fit side-chains REVERT: A 50 ASP cc_start: 0.7428 (t0) cc_final: 0.7133 (t0) REVERT: A 106 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8123 (tt) REVERT: A 203 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7993 (t) REVERT: A 418 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: B 50 ASP cc_start: 0.7497 (t0) cc_final: 0.7183 (t0) REVERT: B 106 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8174 (tt) REVERT: B 418 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7253 (mt-10) REVERT: C 292 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 303 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8841 (mp) REVERT: D 303 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8839 (mp) REVERT: E 207 MET cc_start: 0.8557 (mmm) cc_final: 0.8118 (mmm) REVERT: E 310 GLU cc_start: 0.8269 (pt0) cc_final: 0.8050 (pt0) REVERT: E 362 ASP cc_start: 0.8383 (t0) cc_final: 0.8132 (t70) REVERT: E 439 GLU cc_start: 0.8632 (mp0) cc_final: 0.8025 (mp0) REVERT: F 207 MET cc_start: 0.8585 (mmm) cc_final: 0.8132 (mmm) REVERT: F 310 GLU cc_start: 0.8306 (pt0) cc_final: 0.8096 (pt0) REVERT: F 362 ASP cc_start: 0.8396 (t0) cc_final: 0.8169 (t70) REVERT: F 439 GLU cc_start: 0.8640 (mp0) cc_final: 0.8029 (mp0) REVERT: G 17 ASP cc_start: 0.8298 (t0) cc_final: 0.7883 (t0) REVERT: G 75 PHE cc_start: 0.8866 (t80) cc_final: 0.8293 (t80) REVERT: G 164 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7832 (tpp) REVERT: G 187 MET cc_start: 0.8860 (tpt) cc_final: 0.8561 (tpt) REVERT: G 244 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8273 (tp40) REVERT: H 17 ASP cc_start: 0.8337 (t0) cc_final: 0.8032 (t0) REVERT: H 20 MET cc_start: 0.6113 (ttt) cc_final: 0.5849 (ttt) REVERT: H 75 PHE cc_start: 0.8877 (t80) cc_final: 0.8310 (t80) REVERT: H 164 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7847 (tpp) REVERT: H 244 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8206 (tp40) REVERT: I 102 LEU cc_start: 0.7774 (tt) cc_final: 0.7267 (tt) REVERT: I 206 CYS cc_start: 0.6888 (m) cc_final: 0.6511 (m) REVERT: I 209 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8204 (mmmt) outliers start: 115 outliers final: 82 residues processed: 628 average time/residue: 0.3115 time to fit residues: 326.4381 Evaluate side-chains 634 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 543 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.6980 chunk 137 optimal weight: 0.1980 chunk 204 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 269 optimal weight: 0.1980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN F 470 HIS I 115 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26213 Z= 0.190 Angle : 0.538 7.984 35599 Z= 0.297 Chirality : 0.043 0.173 4387 Planarity : 0.004 0.051 4526 Dihedral : 4.021 30.678 3615 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.29 % Allowed : 22.03 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.34 (0.15), residues: 3555 helix: 1.70 (0.14), residues: 1390 sheet: -0.92 (0.21), residues: 688 loop : -0.56 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 37 HIS 0.008 0.001 HIS J 115 PHE 0.018 0.001 PHE C 177 TYR 0.011 0.001 TYR G 304 ARG 0.001 0.000 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 567 time to evaluate : 3.459 Fit side-chains REVERT: A 50 ASP cc_start: 0.7461 (t0) cc_final: 0.7172 (t0) REVERT: A 106 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8133 (tt) REVERT: A 203 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.8009 (t) REVERT: A 418 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: B 50 ASP cc_start: 0.7505 (t0) cc_final: 0.7202 (t0) REVERT: B 106 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8178 (tt) REVERT: B 203 VAL cc_start: 0.8219 (OUTLIER) cc_final: 0.8000 (t) REVERT: B 418 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: C 68 MET cc_start: 0.8300 (mtp) cc_final: 0.7818 (mtp) REVERT: C 292 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7520 (tm-30) REVERT: D 303 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8828 (mp) REVERT: E 362 ASP cc_start: 0.8388 (t0) cc_final: 0.8149 (t70) REVERT: E 439 GLU cc_start: 0.8619 (mp0) cc_final: 0.8003 (mp0) REVERT: F 362 ASP cc_start: 0.8408 (t0) cc_final: 0.8187 (t70) REVERT: F 439 GLU cc_start: 0.8623 (mp0) cc_final: 0.8012 (mp0) REVERT: G 75 PHE cc_start: 0.8871 (t80) cc_final: 0.8317 (t80) REVERT: G 164 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7889 (tpp) REVERT: G 187 MET cc_start: 0.8856 (tpt) cc_final: 0.8485 (tpt) REVERT: G 244 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8235 (tp40) REVERT: H 17 ASP cc_start: 0.8341 (t0) cc_final: 0.8035 (t0) REVERT: H 20 MET cc_start: 0.6320 (ttt) cc_final: 0.6067 (ttt) REVERT: H 75 PHE cc_start: 0.8877 (t80) cc_final: 0.8333 (t80) REVERT: H 113 ASP cc_start: 0.7742 (m-30) cc_final: 0.7460 (m-30) REVERT: H 164 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7865 (tpp) REVERT: H 244 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8202 (tp40) REVERT: I 102 LEU cc_start: 0.7798 (tt) cc_final: 0.7290 (tt) REVERT: I 206 CYS cc_start: 0.6912 (m) cc_final: 0.6558 (m) REVERT: J 1 MET cc_start: 0.6105 (tpt) cc_final: 0.5739 (tpt) REVERT: J 209 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8277 (mmtt) outliers start: 108 outliers final: 92 residues processed: 610 average time/residue: 0.3258 time to fit residues: 332.2544 Evaluate side-chains 635 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 534 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 156 GLN Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 20.0000 chunk 328 optimal weight: 30.0000 chunk 299 optimal weight: 20.0000 chunk 319 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 288 optimal weight: 20.0000 chunk 302 optimal weight: 20.0000 chunk 318 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 HIS ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN M 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.088 26213 Z= 0.715 Angle : 0.872 11.493 35599 Z= 0.466 Chirality : 0.054 0.317 4387 Planarity : 0.005 0.057 4526 Dihedral : 5.524 31.646 3615 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.65 % Allowed : 21.23 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.67 (0.14), residues: 3555 helix: 0.63 (0.14), residues: 1374 sheet: -1.03 (0.24), residues: 477 loop : -1.12 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 37 HIS 0.009 0.002 HIS A 105 PHE 0.038 0.003 PHE H 285 TYR 0.032 0.003 TYR A 128 ARG 0.002 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 518 time to evaluate : 2.897 Fit side-chains REVERT: A 50 ASP cc_start: 0.7681 (t0) cc_final: 0.7473 (t0) REVERT: A 106 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 270 ASP cc_start: 0.8205 (m-30) cc_final: 0.7854 (m-30) REVERT: A 414 CYS cc_start: 0.8646 (m) cc_final: 0.7966 (m) REVERT: B 50 ASP cc_start: 0.7703 (t0) cc_final: 0.7481 (t0) REVERT: B 106 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8264 (tt) REVERT: B 270 ASP cc_start: 0.8137 (m-30) cc_final: 0.7856 (m-30) REVERT: B 414 CYS cc_start: 0.8585 (m) cc_final: 0.7930 (m) REVERT: C 303 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8939 (mp) REVERT: D 20 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8449 (mm-30) REVERT: D 292 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7842 (tm-30) REVERT: D 303 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8933 (mp) REVERT: E 362 ASP cc_start: 0.8461 (t0) cc_final: 0.8199 (t70) REVERT: E 439 GLU cc_start: 0.8728 (mp0) cc_final: 0.8076 (mp0) REVERT: F 196 MET cc_start: 0.7031 (ttp) cc_final: 0.6014 (ttm) REVERT: F 362 ASP cc_start: 0.8453 (t0) cc_final: 0.8241 (t0) REVERT: F 439 GLU cc_start: 0.8737 (mp0) cc_final: 0.8084 (mp0) REVERT: F 462 ASP cc_start: 0.8693 (m-30) cc_final: 0.8393 (m-30) REVERT: G 17 ASP cc_start: 0.8456 (t0) cc_final: 0.8155 (t0) REVERT: G 75 PHE cc_start: 0.8991 (t80) cc_final: 0.8329 (t80) REVERT: G 164 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.7975 (ttt) REVERT: G 214 GLN cc_start: 0.8478 (pt0) cc_final: 0.8104 (pt0) REVERT: H 17 ASP cc_start: 0.8623 (t0) cc_final: 0.8219 (t0) REVERT: H 20 MET cc_start: 0.6403 (ttt) cc_final: 0.6169 (ttt) REVERT: H 75 PHE cc_start: 0.8987 (t80) cc_final: 0.8331 (t80) REVERT: H 164 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.7982 (ttt) REVERT: H 214 GLN cc_start: 0.8482 (pt0) cc_final: 0.8118 (pt0) REVERT: I 50 GLU cc_start: 0.7793 (tt0) cc_final: 0.7271 (mp0) REVERT: I 102 LEU cc_start: 0.8027 (tt) cc_final: 0.7785 (tt) REVERT: I 125 ASP cc_start: 0.8993 (t0) cc_final: 0.8740 (t0) REVERT: I 206 CYS cc_start: 0.7424 (m) cc_final: 0.7035 (m) REVERT: J 1 MET cc_start: 0.6339 (tpt) cc_final: 0.6083 (tpt) REVERT: J 125 ASP cc_start: 0.8990 (t0) cc_final: 0.8780 (t0) outliers start: 142 outliers final: 106 residues processed: 593 average time/residue: 0.3307 time to fit residues: 329.4020 Evaluate side-chains 607 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 495 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 485 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 GLN Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 2.9990 chunk 338 optimal weight: 40.0000 chunk 206 optimal weight: 0.8980 chunk 160 optimal weight: 0.0980 chunk 235 optimal weight: 0.9980 chunk 354 optimal weight: 9.9990 chunk 326 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS B 101 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 HIS F 470 HIS G 213 ASN H 213 ASN I 115 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26213 Z= 0.204 Angle : 0.593 8.739 35599 Z= 0.322 Chirality : 0.044 0.200 4387 Planarity : 0.004 0.052 4526 Dihedral : 4.583 30.410 3615 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.22 % Allowed : 23.86 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.08 (0.15), residues: 3555 helix: 1.39 (0.14), residues: 1357 sheet: -0.97 (0.22), residues: 568 loop : -0.66 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 51 HIS 0.008 0.001 HIS E 274 PHE 0.019 0.001 PHE D 177 TYR 0.014 0.001 TYR A 128 ARG 0.002 0.000 ARG M 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7110 Ramachandran restraints generated. 3555 Oldfield, 0 Emsley, 3555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 555 time to evaluate : 3.080 Fit side-chains REVERT: A 50 ASP cc_start: 0.7490 (t0) cc_final: 0.7192 (t0) REVERT: A 106 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 423 VAL cc_start: 0.9026 (t) cc_final: 0.8826 (t) REVERT: B 50 ASP cc_start: 0.7532 (t0) cc_final: 0.7220 (t0) REVERT: B 106 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8093 (tt) REVERT: C 49 HIS cc_start: 0.7703 (m90) cc_final: 0.7257 (m90) REVERT: C 292 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 303 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8884 (mp) REVERT: D 20 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8470 (tp30) REVERT: D 48 ASP cc_start: 0.7958 (m-30) cc_final: 0.7392 (m-30) REVERT: D 292 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7423 (tm-30) REVERT: D 303 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8844 (mp) REVERT: E 362 ASP cc_start: 0.8378 (t0) cc_final: 0.8151 (t70) REVERT: E 439 GLU cc_start: 0.8646 (mp0) cc_final: 0.8084 (mp0) REVERT: F 439 GLU cc_start: 0.8655 (mp0) cc_final: 0.8110 (mp0) REVERT: F 462 ASP cc_start: 0.8671 (m-30) cc_final: 0.8373 (m-30) REVERT: G 17 ASP cc_start: 0.8334 (t0) cc_final: 0.8017 (t0) REVERT: G 75 PHE cc_start: 0.8920 (t80) cc_final: 0.8305 (t80) REVERT: H 17 ASP cc_start: 0.8457 (t0) cc_final: 0.8074 (t0) REVERT: H 70 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7962 (tp30) REVERT: H 75 PHE cc_start: 0.8913 (t80) cc_final: 0.8314 (t80) REVERT: H 113 ASP cc_start: 0.7887 (m-30) cc_final: 0.7633 (m-30) REVERT: I 102 LEU cc_start: 0.7554 (tt) cc_final: 0.7022 (tt) REVERT: I 125 ASP cc_start: 0.8896 (t0) cc_final: 0.8621 (t0) REVERT: I 161 ASP cc_start: 0.7361 (t70) cc_final: 0.6928 (p0) REVERT: I 206 CYS cc_start: 0.7149 (m) cc_final: 0.6738 (m) REVERT: J 209 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8098 (mmtt) outliers start: 81 outliers final: 66 residues processed: 587 average time/residue: 0.3137 time to fit residues: 306.4548 Evaluate side-chains 591 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 521 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 230 ASN Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 363 SER Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 156 GLN Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 237 ARG Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 237 ARG Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 272 TRP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 20.0000 chunk 300 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 290 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 HIS I 115 HIS J 115 HIS L 67 ASN M 67 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111396 restraints weight = 47974.517| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.63 r_work: 0.3354 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26213 Z= 0.318 Angle : 0.632 9.190 35599 Z= 0.341 Chirality : 0.046 0.204 4387 Planarity : 0.004 0.053 4526 Dihedral : 4.611 30.931 3615 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.62 % Allowed : 23.82 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.13 (0.15), residues: 3555 helix: 1.40 (0.14), residues: 1362 sheet: -0.76 (0.23), residues: 513 loop : -0.69 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 37 HIS 0.008 0.001 HIS J 115 PHE 0.023 0.002 PHE H 285 TYR 0.018 0.001 TYR A 78 ARG 0.001 0.000 ARG G 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7198.91 seconds wall clock time: 131 minutes 11.41 seconds (7871.41 seconds total)