Starting phenix.real_space_refine on Wed Apr 10 05:09:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/04_2024/7k0o_22605_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/04_2024/7k0o_22605.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/7k0o_22605/04_2024/7k0o_22605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/04_2024/7k0o_22605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/04_2024/7k0o_22605_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/04_2024/7k0o_22605_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= 0.101 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 11986 2.51 5 N 3116 2.21 5 O 3352 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 GLU 62": "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 ARG 233": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 315": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 62": "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 ARG 233": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E ARG 459": "NH1" <-> "NH2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 315": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F GLU 437": "OE1" <-> "OE2" Residue "F ARG 450": "NH1" <-> "NH2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 452": "NH1" <-> "NH2" 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-5288/modules/chem_data/mon_lib" Total number of atoms: 18558 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 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: "E" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 31 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: "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: "F" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 102 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: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PLP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 9.72, per 1000 atoms: 0.52 Number of scatterers: 18558 At special positions: 0 Unit cell: (149.745, 135.675, 118.59, 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 3352 8.00 N 3116 7.00 C 11986 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: 7.43 Conformation dependent library (CDL) restraints added in 3.4 seconds 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 8 sheets defined 47.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 22 through 39 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 167 through 178 removed outlier: 4.191A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (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 322 through 331 removed outlier: 4.678A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.472A 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 377 Processing helix chain 'A' and resid 405 through 422 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: 4.695A pdb=" N TYR B 122 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN B 125 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.708A 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 401 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 434 through 456 removed outlier: 3.887A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 removed outlier: 4.057A 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 23 Processing helix chain 'C' and resid 31 through 54 Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'D' and resid 12 through 18 removed outlier: 4.704A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) 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: 6.023A pdb=" N ASP D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 4.027A 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 137 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 'E' and resid 11 through 19 Processing helix chain 'E' and resid 22 through 39 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 167 through 178 removed outlier: 4.191A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (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 322 through 331 removed outlier: 4.679A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.472A 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 377 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 454 through 472 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 31 through 54 Processing helix chain 'G' and resid 59 through 68 Processing helix chain 'H' and resid 12 through 18 removed outlier: 4.704A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) 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: 6.023A pdb=" N ASP H 90 " --> pdb=" O TRP H 86 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.026A 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 137 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 '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: 4.670A pdb=" N TYR F 122 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN F 125 " --> pdb=" O TYR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 133 No H-bonds generated for 'chain 'F' and resid 131 through 133' Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 238 through 249 removed outlier: 3.708A 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 401 Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 434 through 456 removed outlier: 3.887A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 488 removed outlier: 4.058A 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: 3.607A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N GLU A 245 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ASP A 188 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 383 through 386 Processing sheet with id= C, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.545A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.306A 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 Processing sheet with id= E, first strand: chain 'E' and resid 160 through 164 removed outlier: 3.607A pdb=" N LEU E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE E 184 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL E 243 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE E 186 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N GLU E 245 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ASP E 188 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP E 205 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL E 187 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS E 207 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 383 through 386 Processing sheet with id= G, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.545A pdb=" N LEU F 255 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU F 313 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU F 257 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLU F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR F 276 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER F 258 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.307A 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 472 808 hydrogen bonds defined for protein. 2328 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: 5.24 Time building geometry restraints manager: 7.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 4454 1.45 - 1.57: 10754 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18946 Sorted by residual: bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" O12 POV F 601 " pdb=" P POV F 601 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+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 1.79e+01 bond pdb=" CA PRO B 413 " pdb=" C PRO B 413 " ideal model delta sigma weight residual 1.517 1.547 -0.029 9.30e-03 1.16e+04 1.00e+01 ... (remaining 18941 not shown) Histogram of bond angle deviations from ideal: 96.48 - 103.99: 276 103.99 - 111.50: 8705 111.50 - 119.01: 6525 119.01 - 126.52: 9850 126.52 - 134.03: 248 Bond angle restraints: 25604 Sorted by residual: angle pdb=" C28 POV D 901 " pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 127.79 110.07 17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 110.08 17.71 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 110.03 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 110.05 17.62 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CA PRO F 413 " pdb=" C PRO F 413 " pdb=" N PRO F 414 " ideal model delta sigma weight residual 117.93 124.26 -6.33 1.20e+00 6.94e-01 2.78e+01 ... (remaining 25599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10442 17.80 - 35.60: 746 35.60 - 53.40: 152 53.40 - 71.20: 12 71.20 - 88.99: 14 Dihedral angle restraints: 11366 sinusoidal: 4580 harmonic: 6786 Sorted by residual: dihedral pdb=" CA LYS D 79 " pdb=" C LYS D 79 " pdb=" N ALA D 80 " pdb=" CA ALA D 80 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS H 79 " pdb=" C LYS H 79 " pdb=" N ALA H 80 " pdb=" CA ALA H 80 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA VAL D 93 " pdb=" C VAL D 93 " pdb=" N GLN D 94 " pdb=" CA GLN D 94 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 11363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1882 0.038 - 0.076: 683 0.076 - 0.114: 227 0.114 - 0.152: 56 0.152 - 0.190: 6 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA THR H 105 " pdb=" N THR H 105 " pdb=" C THR H 105 " pdb=" CB THR H 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA THR D 105 " pdb=" N THR D 105 " pdb=" C THR D 105 " pdb=" CB THR D 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA PRO B 413 " pdb=" N PRO B 413 " pdb=" C PRO B 413 " pdb=" CB PRO B 413 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 2851 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 469 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO F 470 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 470 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 470 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO B 470 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 502 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.027 5.00e-02 4.00e+02 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 518 2.71 - 3.26: 18184 3.26 - 3.80: 28806 3.80 - 4.35: 37441 4.35 - 4.90: 65287 Nonbonded interactions: 150236 Sorted by model distance: nonbonded pdb=" O VAL D 10 " pdb=" OG1 THR D 74 " model vdw 2.161 2.440 nonbonded pdb=" O VAL H 10 " pdb=" OG1 THR H 74 " model vdw 2.161 2.440 nonbonded pdb=" OH TYR B 448 " pdb=" OD1 ASP B 522 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR F 448 " pdb=" OD1 ASP F 522 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.266 2.440 ... (remaining 150231 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 544) selection = (chain 'F' and resid 53 through 544) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 1 through 153 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.020 Extract box with map and model: 10.090 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 50.020 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.190 18946 Z= 0.363 Angle : 0.745 17.715 25604 Z= 0.411 Chirality : 0.045 0.190 2854 Planarity : 0.005 0.050 3244 Dihedral : 13.026 88.995 7022 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.21 % Allowed : 0.67 % Favored : 99.12 % 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: 0.95 (0.17), residues: 2326 helix: 1.76 (0.15), residues: 1092 sheet: -0.25 (0.35), residues: 226 loop : -0.38 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 32 HIS 0.007 0.001 HIS E 24 PHE 0.022 0.002 PHE E 168 TYR 0.029 0.002 TYR E 166 ARG 0.014 0.001 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 2.018 Fit side-chains REVERT: A 214 MET cc_start: 0.6571 (mmt) cc_final: 0.6189 (mmt) REVERT: B 285 MET cc_start: 0.8032 (mmt) cc_final: 0.7384 (mmt) REVERT: E 214 MET cc_start: 0.6508 (mmt) cc_final: 0.6166 (mmt) REVERT: F 285 MET cc_start: 0.7993 (mmt) cc_final: 0.7333 (mmt) outliers start: 4 outliers final: 0 residues processed: 233 average time/residue: 0.3517 time to fit residues: 120.9689 Evaluate side-chains 193 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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: 3.9990 chunk 175 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18946 Z= 0.222 Angle : 0.510 7.230 25604 Z= 0.271 Chirality : 0.042 0.181 2854 Planarity : 0.005 0.048 3244 Dihedral : 6.835 65.314 2710 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.62 % Allowed : 6.93 % Favored : 92.45 % 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: 1.13 (0.17), residues: 2326 helix: 1.97 (0.15), residues: 1094 sheet: -0.24 (0.35), residues: 226 loop : -0.35 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 32 HIS 0.005 0.001 HIS H 143 PHE 0.016 0.002 PHE E 168 TYR 0.015 0.001 TYR A 166 ARG 0.004 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 2.228 Fit side-chains REVERT: A 55 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8444 (pttp) REVERT: B 285 MET cc_start: 0.7926 (mmt) cc_final: 0.7368 (mmt) REVERT: D 79 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8027 (tppt) REVERT: E 55 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8443 (pttp) REVERT: H 79 LYS cc_start: 0.8369 (mmmm) cc_final: 0.7953 (tppt) REVERT: F 285 MET cc_start: 0.7897 (mmt) cc_final: 0.7334 (mmt) outliers start: 12 outliers final: 12 residues processed: 212 average time/residue: 0.3375 time to fit residues: 107.5398 Evaluate side-chains 208 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 175 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 211 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 169 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18946 Z= 0.143 Angle : 0.449 6.366 25604 Z= 0.238 Chirality : 0.040 0.170 2854 Planarity : 0.004 0.085 3244 Dihedral : 6.236 66.458 2710 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.14 % Allowed : 7.29 % Favored : 91.57 % 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: 1.40 (0.17), residues: 2326 helix: 2.14 (0.15), residues: 1114 sheet: 0.07 (0.33), residues: 250 loop : -0.24 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.003 0.000 HIS F 403 PHE 0.014 0.001 PHE E 168 TYR 0.009 0.001 TYR E 166 ARG 0.004 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 216 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.8333 (mt) cc_final: 0.7693 (mt) REVERT: B 285 MET cc_start: 0.7695 (mmt) cc_final: 0.7294 (mmt) REVERT: D 113 THR cc_start: 0.7955 (t) cc_final: 0.7653 (p) REVERT: D 119 TYR cc_start: 0.7238 (m-80) cc_final: 0.6773 (m-80) REVERT: E 260 LEU cc_start: 0.8341 (mt) cc_final: 0.7682 (mt) REVERT: H 113 THR cc_start: 0.7883 (t) cc_final: 0.7641 (p) REVERT: F 285 MET cc_start: 0.7722 (mmt) cc_final: 0.7316 (mmt) outliers start: 22 outliers final: 8 residues processed: 232 average time/residue: 0.3212 time to fit residues: 112.0321 Evaluate side-chains 206 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 0.0000 chunk 141 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 428 GLN E 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18946 Z= 0.175 Angle : 0.466 6.939 25604 Z= 0.247 Chirality : 0.041 0.168 2854 Planarity : 0.005 0.077 3244 Dihedral : 6.088 65.191 2710 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.98 % Allowed : 9.72 % Favored : 89.30 % 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: 1.48 (0.18), residues: 2326 helix: 2.26 (0.15), residues: 1100 sheet: 0.12 (0.33), residues: 250 loop : -0.24 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS F 403 PHE 0.014 0.001 PHE E 168 TYR 0.011 0.001 TYR E 164 ARG 0.005 0.000 ARG E 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 202 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7693 (tp40) cc_final: 0.7365 (tt0) REVERT: B 152 GLN cc_start: 0.8680 (mt0) cc_final: 0.8450 (mt0) REVERT: D 113 THR cc_start: 0.7984 (t) cc_final: 0.7677 (p) REVERT: E 407 GLN cc_start: 0.7690 (tp40) cc_final: 0.7353 (tt0) REVERT: H 113 THR cc_start: 0.7959 (t) cc_final: 0.7702 (p) outliers start: 19 outliers final: 13 residues processed: 217 average time/residue: 0.3245 time to fit residues: 106.4428 Evaluate side-chains 205 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 0.0670 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 114 optimal weight: 0.1980 chunk 201 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN E 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18946 Z= 0.174 Angle : 0.461 7.275 25604 Z= 0.243 Chirality : 0.041 0.166 2854 Planarity : 0.004 0.070 3244 Dihedral : 6.016 65.908 2710 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.65 % Allowed : 9.82 % Favored : 88.52 % 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: 1.49 (0.18), residues: 2326 helix: 2.26 (0.15), residues: 1102 sheet: 0.13 (0.33), residues: 250 loop : -0.24 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.003 0.001 HIS F 403 PHE 0.016 0.001 PHE D 115 TYR 0.011 0.001 TYR A 164 ARG 0.001 0.000 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7641 (tp40) cc_final: 0.7288 (tt0) REVERT: B 126 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8623 (tt) REVERT: B 281 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8474 (mptt) REVERT: B 285 MET cc_start: 0.7618 (mmt) cc_final: 0.7135 (mmt) REVERT: D 113 THR cc_start: 0.8012 (t) cc_final: 0.7725 (p) REVERT: E 407 GLN cc_start: 0.7671 (tp40) cc_final: 0.7321 (tt0) REVERT: H 113 THR cc_start: 0.7975 (t) cc_final: 0.7713 (p) REVERT: F 126 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8582 (tt) REVERT: F 281 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8448 (mptt) REVERT: F 285 MET cc_start: 0.7631 (mmt) cc_final: 0.7129 (mmt) outliers start: 32 outliers final: 23 residues processed: 229 average time/residue: 0.3325 time to fit residues: 114.8545 Evaluate side-chains 219 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18946 Z= 0.259 Angle : 0.509 6.574 25604 Z= 0.268 Chirality : 0.043 0.168 2854 Planarity : 0.005 0.070 3244 Dihedral : 6.180 66.216 2710 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.76 % Allowed : 10.75 % Favored : 87.49 % 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: 1.30 (0.17), residues: 2326 helix: 2.11 (0.15), residues: 1102 sheet: -0.02 (0.33), residues: 250 loop : -0.32 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.005 0.001 HIS F 403 PHE 0.016 0.002 PHE E 168 TYR 0.014 0.001 TYR A 164 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 200 time to evaluate : 2.323 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7555 (tp40) cc_final: 0.7198 (tt0) REVERT: B 126 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8604 (tt) REVERT: B 281 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8464 (mptt) REVERT: B 285 MET cc_start: 0.7754 (mmt) cc_final: 0.7238 (mmt) REVERT: D 79 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8170 (tttm) REVERT: D 113 THR cc_start: 0.8037 (t) cc_final: 0.7724 (p) REVERT: E 407 GLN cc_start: 0.7580 (tp40) cc_final: 0.7225 (tt0) REVERT: H 113 THR cc_start: 0.8026 (t) cc_final: 0.7732 (p) REVERT: F 126 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8652 (tt) REVERT: F 281 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8462 (mptt) REVERT: F 285 MET cc_start: 0.7748 (mmt) cc_final: 0.7229 (mmt) outliers start: 34 outliers final: 24 residues processed: 226 average time/residue: 0.3364 time to fit residues: 114.7122 Evaluate side-chains 220 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18946 Z= 0.196 Angle : 0.483 8.595 25604 Z= 0.255 Chirality : 0.041 0.165 2854 Planarity : 0.005 0.068 3244 Dihedral : 6.069 66.969 2710 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.02 % Allowed : 11.74 % Favored : 86.25 % 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: 1.38 (0.17), residues: 2326 helix: 2.19 (0.15), residues: 1098 sheet: -0.01 (0.33), residues: 250 loop : -0.27 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 PHE 0.018 0.001 PHE H 115 TYR 0.011 0.001 TYR E 164 ARG 0.003 0.000 ARG E 459 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 2.179 Fit side-chains REVERT: A 407 GLN cc_start: 0.7540 (tp40) cc_final: 0.7132 (tt0) REVERT: B 126 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8561 (tt) REVERT: B 281 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8469 (mptt) REVERT: B 285 MET cc_start: 0.7612 (mmt) cc_final: 0.7111 (mmt) REVERT: D 79 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8210 (tttm) REVERT: D 113 THR cc_start: 0.8025 (t) cc_final: 0.7728 (p) REVERT: E 407 GLN cc_start: 0.7548 (tp40) cc_final: 0.7139 (tt0) REVERT: H 79 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8171 (tttm) REVERT: H 113 THR cc_start: 0.7995 (t) cc_final: 0.7712 (p) REVERT: F 126 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8581 (tt) REVERT: F 281 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8468 (mptt) REVERT: F 285 MET cc_start: 0.7586 (mmt) cc_final: 0.7098 (mmt) outliers start: 39 outliers final: 27 residues processed: 231 average time/residue: 0.3339 time to fit residues: 117.3912 Evaluate side-chains 228 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.0010 chunk 142 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.0070 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN E 229 GLN ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18946 Z= 0.150 Angle : 0.458 8.662 25604 Z= 0.243 Chirality : 0.040 0.162 2854 Planarity : 0.004 0.065 3244 Dihedral : 5.887 66.929 2710 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.07 % Allowed : 12.05 % Favored : 85.88 % 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: 1.50 (0.18), residues: 2326 helix: 2.29 (0.15), residues: 1102 sheet: 0.09 (0.33), residues: 250 loop : -0.24 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 32 HIS 0.004 0.000 HIS E 24 PHE 0.014 0.001 PHE E 168 TYR 0.009 0.001 TYR E 164 ARG 0.004 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 200 time to evaluate : 2.203 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7592 (tp40) cc_final: 0.7179 (tt0) REVERT: B 126 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8538 (tt) REVERT: B 281 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8481 (mptt) REVERT: B 285 MET cc_start: 0.7632 (mmt) cc_final: 0.7139 (mmt) REVERT: D 79 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8160 (tttm) REVERT: D 113 THR cc_start: 0.7997 (t) cc_final: 0.7729 (p) REVERT: E 407 GLN cc_start: 0.7597 (tp40) cc_final: 0.7186 (tt0) REVERT: H 79 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8140 (tttm) REVERT: H 113 THR cc_start: 0.7970 (t) cc_final: 0.7712 (p) REVERT: F 126 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8581 (tt) REVERT: F 281 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8480 (mptt) REVERT: F 285 MET cc_start: 0.7626 (mmt) cc_final: 0.7129 (mmt) outliers start: 40 outliers final: 30 residues processed: 231 average time/residue: 0.3354 time to fit residues: 117.6253 Evaluate side-chains 227 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 214 optimal weight: 0.0060 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 0.0470 chunk 197 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 overall best weight: 0.5294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 441 GLN E 229 GLN F 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18946 Z= 0.153 Angle : 0.463 8.539 25604 Z= 0.245 Chirality : 0.041 0.162 2854 Planarity : 0.004 0.065 3244 Dihedral : 5.839 66.853 2710 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.86 % Allowed : 12.25 % Favored : 85.88 % 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: 1.48 (0.18), residues: 2326 helix: 2.28 (0.15), residues: 1114 sheet: -0.01 (0.35), residues: 226 loop : -0.26 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.003 0.000 HIS E 24 PHE 0.019 0.001 PHE H 115 TYR 0.009 0.001 TYR A 164 ARG 0.004 0.000 ARG E 459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7532 (tp40) cc_final: 0.7108 (tt0) REVERT: B 126 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8536 (tt) REVERT: B 281 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8484 (mptt) REVERT: B 285 MET cc_start: 0.7603 (mmt) cc_final: 0.7130 (mmt) REVERT: D 79 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8177 (tttm) REVERT: D 113 THR cc_start: 0.7991 (t) cc_final: 0.7695 (p) REVERT: E 407 GLN cc_start: 0.7555 (tp40) cc_final: 0.7131 (tt0) REVERT: H 79 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8156 (tttm) REVERT: H 113 THR cc_start: 0.7974 (t) cc_final: 0.7718 (p) REVERT: F 126 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8588 (tt) REVERT: F 281 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8484 (mptt) REVERT: F 285 MET cc_start: 0.7600 (mmt) cc_final: 0.7119 (mmt) outliers start: 36 outliers final: 28 residues processed: 225 average time/residue: 0.3312 time to fit residues: 111.6545 Evaluate side-chains 224 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN F 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18946 Z= 0.272 Angle : 0.527 9.118 25604 Z= 0.277 Chirality : 0.044 0.168 2854 Planarity : 0.005 0.067 3244 Dihedral : 6.127 68.656 2710 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.96 % Allowed : 12.10 % Favored : 85.94 % 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: 1.22 (0.17), residues: 2326 helix: 2.08 (0.15), residues: 1100 sheet: -0.20 (0.35), residues: 226 loop : -0.37 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 32 HIS 0.006 0.001 HIS E 24 PHE 0.018 0.002 PHE A 168 TYR 0.015 0.001 TYR E 164 ARG 0.005 0.000 ARG B 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 2.093 Fit side-chains revert: symmetry clash REVERT: B 126 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8600 (tt) REVERT: B 152 GLN cc_start: 0.8655 (mt0) cc_final: 0.8418 (mt0) REVERT: B 281 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8479 (mptt) REVERT: B 285 MET cc_start: 0.7779 (mmt) cc_final: 0.7237 (mmt) REVERT: D 79 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8304 (tttm) REVERT: D 113 THR cc_start: 0.8056 (t) cc_final: 0.7746 (p) REVERT: E 25 LEU cc_start: 0.7147 (mm) cc_final: 0.6832 (mp) REVERT: E 407 GLN cc_start: 0.7543 (tp40) cc_final: 0.7137 (tt0) REVERT: H 79 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8292 (tttm) REVERT: H 113 THR cc_start: 0.8035 (t) cc_final: 0.7730 (p) REVERT: F 126 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8611 (tt) REVERT: F 152 GLN cc_start: 0.8648 (mt0) cc_final: 0.8412 (mt0) REVERT: F 281 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8480 (mptt) REVERT: F 285 MET cc_start: 0.7774 (mmt) cc_final: 0.7229 (mmt) outliers start: 38 outliers final: 30 residues processed: 224 average time/residue: 0.3358 time to fit residues: 113.0428 Evaluate side-chains 229 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 441 GLN E 229 GLN F 441 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112651 restraints weight = 23046.850| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.55 r_work: 0.3059 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18946 Z= 0.184 Angle : 0.482 8.665 25604 Z= 0.255 Chirality : 0.041 0.164 2854 Planarity : 0.005 0.066 3244 Dihedral : 5.980 68.486 2710 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.81 % Allowed : 12.56 % Favored : 85.63 % 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: 1.29 (0.17), residues: 2326 helix: 2.10 (0.15), residues: 1112 sheet: -0.16 (0.36), residues: 226 loop : -0.30 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 PHE 0.019 0.001 PHE H 115 TYR 0.011 0.001 TYR E 164 ARG 0.003 0.000 ARG A 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4029.01 seconds wall clock time: 74 minutes 40.49 seconds (4480.49 seconds total)