Starting phenix.real_space_refine on Sun Mar 17 17:43:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0n_22604/03_2024/7k0n_22604_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0n_22604/03_2024/7k0n_22604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0n_22604/03_2024/7k0n_22604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0n_22604/03_2024/7k0n_22604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0n_22604/03_2024/7k0n_22604_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0n_22604/03_2024/7k0n_22604_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.103 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 4 5.49 5 S 100 5.16 5 C 11952 2.51 5 N 3090 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E GLU 274": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 454": "OE1" <-> "OE2" Residue "E ARG 459": "NH1" <-> "NH2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 304": "NH1" <-> "NH2" Residue "F ARG 305": "NH1" <-> "NH2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F ARG 450": "NH1" <-> "NH2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 452": "NH1" <-> "NH2" Residue "F GLU 464": "OE1" <-> "OE2" Residue "F ARG 484": "NH1" <-> "NH2" Residue "F ARG 507": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18470 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3550 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3857 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 473} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3550 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "F" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3857 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 473} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 9.88, per 1000 atoms: 0.53 Number of scatterers: 18470 At special positions: 0 Unit cell: (151.755, 115.575, 117.585, 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 100 16.00 P 4 15.00 O 3324 8.00 N 3090 7.00 C 11952 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.66 Conformation dependent library (CDL) restraints added in 3.3 seconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 8 sheets defined 47.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 22 through 40 removed outlier: 3.605A pdb=" N PHE A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.579A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 167 through 178 removed outlier: 4.633A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 322 through 331 removed outlier: 4.844A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 361 through 376 Processing helix chain 'A' and resid 405 through 422 removed outlier: 3.557A pdb=" N ARG A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 472 Processing helix chain 'B' and resid 68 through 93 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 117 through 125 removed outlier: 4.881A pdb=" N TYR B 122 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 125 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.551A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.674A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 285 through 298 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 392 through 400 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 434 through 455 removed outlier: 3.722A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 removed outlier: 4.165A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 31 through 54 Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'D' and resid 22 through 38 Processing helix chain 'D' and resid 45 through 65 Processing helix chain 'D' and resid 85 through 92 removed outlier: 5.980A pdb=" N ASP D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 121 through 138 Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'H' and resid 22 through 38 Processing helix chain 'H' and resid 45 through 65 Processing helix chain 'H' and resid 85 through 92 removed outlier: 5.980A pdb=" N ASP H 90 " --> pdb=" O TRP H 86 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 116 Proline residue: H 106 - end of helix Processing helix chain 'H' and resid 121 through 138 Proline residue: H 137 - end of helix Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 31 through 54 Processing helix chain 'G' and resid 60 through 68 Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 22 through 40 removed outlier: 3.605A pdb=" N PHE E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.580A pdb=" N LYS E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 167 through 178 removed outlier: 4.634A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 172 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 193 through 201 Processing helix chain 'E' and resid 214 through 230 Processing helix chain 'E' and resid 232 through 235 No H-bonds generated for 'chain 'E' and resid 232 through 235' Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 322 through 331 removed outlier: 4.844A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 358 Processing helix chain 'E' and resid 361 through 376 Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.556A pdb=" N ARG E 422 " --> pdb=" O GLN E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 472 Processing helix chain 'F' and resid 68 through 93 Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 117 through 125 removed outlier: 4.897A pdb=" N TYR F 122 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN F 125 " --> pdb=" O TYR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 3.551A pdb=" N ARG F 131 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP F 132 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 198 Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 238 through 249 removed outlier: 3.675A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 285 through 298 Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'F' and resid 359 through 363 Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 392 through 400 Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'F' and resid 413 through 426 Processing helix chain 'F' and resid 434 through 455 removed outlier: 3.722A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 488 removed outlier: 4.166A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 535 Processing sheet with id= A, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.638A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLU A 245 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP A 188 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 393 through 397 Processing sheet with id= C, first strand: chain 'B' and resid 231 through 235 removed outlier: 4.206A pdb=" N THR B 376 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.819A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 160 through 164 removed outlier: 3.638A pdb=" N LEU E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE E 184 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL E 243 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE E 186 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLU E 245 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP E 188 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP E 205 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL E 187 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS E 207 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 393 through 397 Processing sheet with id= G, first strand: chain 'F' and resid 231 through 235 removed outlier: 4.206A pdb=" N THR F 376 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU F 255 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU F 313 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU F 257 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR F 276 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER F 258 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG F 278 " --> pdb=" O SER F 258 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 7.22 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: 5793 1.34 - 1.46: 2665 1.46 - 1.57: 10222 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18852 Sorted by residual: bond pdb=" C29 POV H 903 " pdb="C210 POV H 903 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" C29 POV D 903 " pdb="C210 POV D 903 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O12 POV F 602 " pdb=" P POV F 602 " ideal model delta sigma weight residual 1.657 1.741 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N ASN F 120 " pdb=" CA ASN F 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 6.95e+00 ... (remaining 18847 not shown) Histogram of bond angle deviations from ideal: 96.22 - 103.78: 276 103.78 - 111.34: 8115 111.34 - 118.89: 6984 118.89 - 126.45: 9850 126.45 - 134.01: 251 Bond angle restraints: 25476 Sorted by residual: angle pdb=" C29 POV D 903 " pdb="C210 POV D 903 " pdb="C211 POV D 903 " ideal model delta sigma weight residual 127.67 109.58 18.09 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C29 POV H 903 " pdb="C210 POV H 903 " pdb="C211 POV H 903 " ideal model delta sigma weight residual 127.67 109.60 18.07 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C28 POV H 903 " pdb=" C29 POV H 903 " pdb="C210 POV H 903 " ideal model delta sigma weight residual 127.79 110.40 17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" C28 POV D 903 " pdb=" C29 POV D 903 " pdb="C210 POV D 903 " ideal model delta sigma weight residual 127.79 110.42 17.37 3.00e+00 1.11e-01 3.35e+01 angle pdb=" N VAL E 450 " pdb=" CA VAL E 450 " pdb=" C VAL E 450 " ideal model delta sigma weight residual 112.80 108.66 4.14 1.15e+00 7.56e-01 1.29e+01 ... (remaining 25471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 10610 22.97 - 45.93: 600 45.93 - 68.90: 62 68.90 - 91.87: 24 91.87 - 114.84: 2 Dihedral angle restraints: 11298 sinusoidal: 4518 harmonic: 6780 Sorted by residual: dihedral pdb=" C5A PLP F 603 " pdb=" O4P PLP F 603 " pdb=" P PLP F 603 " pdb=" O1P PLP F 603 " ideal model delta sinusoidal sigma weight residual 76.43 -168.74 -114.84 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -168.74 -114.83 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA ASN B 133 " pdb=" C ASN B 133 " pdb=" N TRP B 134 " pdb=" CA TRP B 134 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 11295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1757 0.029 - 0.058: 651 0.058 - 0.087: 246 0.087 - 0.117: 161 0.117 - 0.146: 31 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CB THR H 52 " pdb=" CA THR H 52 " pdb=" OG1 THR H 52 " pdb=" CG2 THR H 52 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CB THR D 52 " pdb=" CA THR D 52 " pdb=" OG1 THR D 52 " pdb=" CG2 THR D 52 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE E 242 " pdb=" N ILE E 242 " pdb=" C ILE E 242 " pdb=" CB ILE E 242 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 2843 not shown) Planarity restraints: 3224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV H 903 " 0.080 2.00e-02 2.50e+03 8.01e-02 6.42e+01 pdb=" C29 POV H 903 " -0.082 2.00e-02 2.50e+03 pdb="C210 POV H 903 " -0.079 2.00e-02 2.50e+03 pdb="C211 POV H 903 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 903 " -0.080 2.00e-02 2.50e+03 8.01e-02 6.42e+01 pdb=" C29 POV D 903 " 0.082 2.00e-02 2.50e+03 pdb="C210 POV D 903 " 0.079 2.00e-02 2.50e+03 pdb="C211 POV D 903 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 413 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.030 5.00e-02 4.00e+02 ... (remaining 3221 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3042 2.76 - 3.30: 17173 3.30 - 3.83: 29551 3.83 - 4.37: 35912 4.37 - 4.90: 63059 Nonbonded interactions: 148737 Sorted by model distance: nonbonded pdb=" O TRP E 64 " pdb=" NZ LYS F 338 " model vdw 2.227 2.520 nonbonded pdb=" O VAL H 10 " pdb=" OG1 THR H 74 " model vdw 2.232 2.440 nonbonded pdb=" O VAL D 10 " pdb=" OG1 THR D 74 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.243 2.440 ... (remaining 148732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 53 through 543 or resid 602)) selection = (chain 'F' and (resid 53 through 543 or resid 602)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.010 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 47.240 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 18852 Z= 0.220 Angle : 0.688 18.087 25476 Z= 0.378 Chirality : 0.042 0.146 2846 Planarity : 0.004 0.080 3224 Dihedral : 14.059 114.836 6958 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.32 % Allowed : 0.47 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.17), residues: 2324 helix: 1.74 (0.15), residues: 1116 sheet: -0.44 (0.36), residues: 220 loop : -0.76 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 32 HIS 0.008 0.001 HIS E 24 PHE 0.011 0.001 PHE F 239 TYR 0.020 0.001 TYR A 166 ARG 0.007 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 222 time to evaluate : 2.042 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 224 average time/residue: 0.3308 time to fit residues: 110.1047 Evaluate side-chains 179 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 0.0040 chunk 135 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18852 Z= 0.169 Angle : 0.483 8.826 25476 Z= 0.252 Chirality : 0.041 0.135 2846 Planarity : 0.004 0.051 3224 Dihedral : 7.653 82.524 2718 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.95 % Allowed : 5.88 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.17), residues: 2324 helix: 1.87 (0.15), residues: 1136 sheet: -0.43 (0.36), residues: 220 loop : -0.66 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 PHE 0.014 0.001 PHE F 111 TYR 0.015 0.001 TYR A 166 ARG 0.003 0.000 ARG F 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 2.100 Fit side-chains REVERT: B 434 LEU cc_start: 0.6840 (tp) cc_final: 0.6613 (mp) outliers start: 18 outliers final: 11 residues processed: 196 average time/residue: 0.3425 time to fit residues: 99.8133 Evaluate side-chains 190 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain F residue 110 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 209 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 94 GLN H 77 GLN H 94 GLN E 469 GLN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18852 Z= 0.220 Angle : 0.495 8.752 25476 Z= 0.259 Chirality : 0.042 0.140 2846 Planarity : 0.004 0.053 3224 Dihedral : 7.233 67.846 2718 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.52 % Allowed : 8.19 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.17), residues: 2324 helix: 1.84 (0.15), residues: 1126 sheet: -0.45 (0.36), residues: 220 loop : -0.63 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 32 HIS 0.005 0.001 HIS E 24 PHE 0.016 0.002 PHE B 111 TYR 0.018 0.001 TYR C 27 ARG 0.003 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 2.015 Fit side-chains outliers start: 29 outliers final: 26 residues processed: 207 average time/residue: 0.3245 time to fit residues: 100.7436 Evaluate side-chains 204 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18852 Z= 0.305 Angle : 0.548 9.071 25476 Z= 0.285 Chirality : 0.044 0.153 2846 Planarity : 0.004 0.054 3224 Dihedral : 7.299 64.201 2718 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.52 % Allowed : 10.24 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.17), residues: 2324 helix: 1.67 (0.15), residues: 1122 sheet: -0.58 (0.37), residues: 220 loop : -0.76 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 32 HIS 0.007 0.001 HIS A 24 PHE 0.015 0.002 PHE A 317 TYR 0.020 0.002 TYR E 166 ARG 0.003 0.000 ARG F 484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 2.010 Fit side-chains REVERT: A 469 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6626 (mp-120) REVERT: E 469 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6633 (mp-120) outliers start: 29 outliers final: 22 residues processed: 201 average time/residue: 0.3137 time to fit residues: 95.0851 Evaluate side-chains 203 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 114 optimal weight: 0.5980 chunk 201 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18852 Z= 0.157 Angle : 0.459 9.910 25476 Z= 0.239 Chirality : 0.041 0.137 2846 Planarity : 0.004 0.051 3224 Dihedral : 6.795 58.586 2718 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.47 % Allowed : 11.19 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.18), residues: 2324 helix: 1.89 (0.15), residues: 1124 sheet: -0.62 (0.37), residues: 224 loop : -0.70 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS A 24 PHE 0.012 0.001 PHE F 280 TYR 0.020 0.001 TYR C 27 ARG 0.002 0.000 ARG F 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 2.065 Fit side-chains REVERT: A 469 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6584 (mp-120) REVERT: G 50 TYR cc_start: 0.7338 (t80) cc_final: 0.6826 (t80) REVERT: E 469 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6589 (mp-120) outliers start: 28 outliers final: 23 residues processed: 204 average time/residue: 0.3185 time to fit residues: 98.5021 Evaluate side-chains 207 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.4980 chunk 201 optimal weight: 0.6980 chunk 44 optimal weight: 0.0770 chunk 131 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.0370 chunk 117 optimal weight: 0.0770 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18852 Z= 0.117 Angle : 0.421 6.772 25476 Z= 0.219 Chirality : 0.039 0.133 2846 Planarity : 0.003 0.049 3224 Dihedral : 6.293 59.715 2718 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.58 % Allowed : 11.55 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.12 (0.18), residues: 2324 helix: 2.10 (0.16), residues: 1122 sheet: -0.36 (0.38), residues: 224 loop : -0.59 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 32 HIS 0.003 0.000 HIS A 24 PHE 0.009 0.001 PHE F 280 TYR 0.019 0.001 TYR C 27 ARG 0.001 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 2.367 Fit side-chains REVERT: A 263 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 469 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6592 (mp-120) REVERT: G 50 TYR cc_start: 0.7228 (t80) cc_final: 0.6822 (t80) REVERT: E 263 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8207 (mp) REVERT: E 356 MET cc_start: 0.8825 (mtp) cc_final: 0.8546 (ttm) REVERT: E 469 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6597 (mp-120) REVERT: F 155 ASP cc_start: 0.8303 (t0) cc_final: 0.8068 (t0) outliers start: 30 outliers final: 20 residues processed: 229 average time/residue: 0.3055 time to fit residues: 106.3567 Evaluate side-chains 217 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 127 optimal weight: 0.0060 chunk 163 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18852 Z= 0.166 Angle : 0.458 11.740 25476 Z= 0.235 Chirality : 0.041 0.135 2846 Planarity : 0.004 0.049 3224 Dihedral : 6.297 59.195 2718 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 12.03 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.18), residues: 2324 helix: 2.05 (0.16), residues: 1122 sheet: -0.46 (0.37), residues: 224 loop : -0.61 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.004 0.001 HIS B 403 PHE 0.010 0.001 PHE A 317 TYR 0.018 0.001 TYR C 27 ARG 0.007 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 2.202 Fit side-chains REVERT: A 263 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8211 (mp) REVERT: A 469 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6618 (mp-120) REVERT: E 263 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8236 (mp) REVERT: E 469 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6622 (mp-120) REVERT: F 155 ASP cc_start: 0.8343 (t0) cc_final: 0.8083 (t0) outliers start: 29 outliers final: 22 residues processed: 208 average time/residue: 0.3057 time to fit residues: 97.5575 Evaluate side-chains 212 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 142 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 0.1980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18852 Z= 0.122 Angle : 0.427 10.361 25476 Z= 0.220 Chirality : 0.040 0.131 2846 Planarity : 0.003 0.049 3224 Dihedral : 6.156 59.806 2718 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.37 % Allowed : 12.13 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.18), residues: 2324 helix: 2.15 (0.16), residues: 1122 sheet: -0.38 (0.37), residues: 224 loop : -0.54 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.003 0.000 HIS A 24 PHE 0.009 0.001 PHE F 280 TYR 0.019 0.001 TYR C 27 ARG 0.006 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 2.073 Fit side-chains REVERT: A 263 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 469 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.6614 (mp-120) REVERT: B 155 ASP cc_start: 0.8244 (t0) cc_final: 0.7997 (t0) REVERT: G 50 TYR cc_start: 0.7237 (t80) cc_final: 0.6868 (t80) REVERT: E 263 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8223 (mp) REVERT: E 469 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.6654 (mp-120) REVERT: F 155 ASP cc_start: 0.8312 (t0) cc_final: 0.8049 (t0) outliers start: 26 outliers final: 21 residues processed: 216 average time/residue: 0.3025 time to fit residues: 100.1405 Evaluate side-chains 217 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18852 Z= 0.267 Angle : 0.516 11.131 25476 Z= 0.266 Chirality : 0.043 0.142 2846 Planarity : 0.004 0.052 3224 Dihedral : 6.510 59.270 2718 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.63 % Allowed : 11.97 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.18), residues: 2324 helix: 1.83 (0.15), residues: 1134 sheet: -0.52 (0.37), residues: 220 loop : -0.68 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.005 0.001 HIS B 403 PHE 0.014 0.002 PHE E 168 TYR 0.021 0.002 TYR C 27 ARG 0.005 0.000 ARG E 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 2.420 Fit side-chains REVERT: A 263 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 469 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6654 (mp-120) REVERT: B 155 ASP cc_start: 0.8434 (t0) cc_final: 0.8162 (t0) REVERT: C 50 TYR cc_start: 0.7210 (t80) cc_final: 0.6734 (t80) REVERT: E 263 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8233 (mp) REVERT: E 469 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6659 (mp-120) REVERT: F 155 ASP cc_start: 0.8502 (t0) cc_final: 0.8192 (t0) outliers start: 31 outliers final: 24 residues processed: 200 average time/residue: 0.3001 time to fit residues: 92.1587 Evaluate side-chains 211 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 chunk 212 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18852 Z= 0.182 Angle : 0.477 11.747 25476 Z= 0.245 Chirality : 0.041 0.135 2846 Planarity : 0.004 0.050 3224 Dihedral : 6.430 58.368 2718 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.52 % Allowed : 12.29 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.18), residues: 2324 helix: 1.93 (0.15), residues: 1122 sheet: -0.61 (0.37), residues: 224 loop : -0.68 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.004 0.001 HIS A 24 PHE 0.011 0.001 PHE E 317 TYR 0.022 0.001 TYR C 27 ARG 0.006 0.000 ARG E 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 2.084 Fit side-chains REVERT: A 263 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8209 (mp) REVERT: A 469 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.6638 (mp-120) REVERT: B 155 ASP cc_start: 0.8420 (t0) cc_final: 0.8143 (t0) REVERT: C 50 TYR cc_start: 0.7262 (t80) cc_final: 0.6747 (t80) REVERT: G 50 TYR cc_start: 0.7283 (t80) cc_final: 0.6851 (t80) REVERT: E 263 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8209 (mp) REVERT: E 469 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6675 (mp-120) REVERT: F 155 ASP cc_start: 0.8488 (t0) cc_final: 0.8176 (t0) outliers start: 29 outliers final: 24 residues processed: 207 average time/residue: 0.3002 time to fit residues: 95.5897 Evaluate side-chains 216 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 169 optimal weight: 0.0270 chunk 27 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 184 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 189 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 overall best weight: 0.1616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.166637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.143587 restraints weight = 22860.607| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.81 r_work: 0.3731 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18852 Z= 0.112 Angle : 0.434 11.857 25476 Z= 0.221 Chirality : 0.039 0.131 2846 Planarity : 0.003 0.048 3224 Dihedral : 6.108 59.943 2718 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.10 % Allowed : 12.55 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.18), residues: 2324 helix: 2.10 (0.16), residues: 1132 sheet: -0.44 (0.37), residues: 224 loop : -0.51 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 32 HIS 0.003 0.000 HIS F 347 PHE 0.007 0.001 PHE H 101 TYR 0.020 0.001 TYR C 27 ARG 0.006 0.000 ARG A 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3741.00 seconds wall clock time: 68 minutes 24.21 seconds (4104.21 seconds total)