Starting phenix.real_space_refine on Thu Mar 21 14:52:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yph_34000/03_2024/7yph_34000_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yph_34000/03_2024/7yph_34000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yph_34000/03_2024/7yph_34000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yph_34000/03_2024/7yph_34000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yph_34000/03_2024/7yph_34000_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yph_34000/03_2024/7yph_34000_updated.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 107 5.16 5 C 19180 2.51 5 N 5345 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 250": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 503": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 519": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "D ARG 503": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 519": "NH1" <-> "NH2" Residue "D ARG 529": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D GLU 749": "OE1" <-> "OE2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 212": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 250": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "E ASP 422": "OD1" <-> "OD2" Residue "E PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 479": "NH1" <-> "NH2" Residue "E ARG 503": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E ARG 519": "NH1" <-> "NH2" Residue "E ARG 529": "NH1" <-> "NH2" Residue "E ARG 567": "NH1" <-> "NH2" Residue "E ARG 584": "NH1" <-> "NH2" Residue "E ARG 693": "NH1" <-> "NH2" Residue "E ARG 694": "NH1" <-> "NH2" Residue "E GLU 744": "OE1" <-> "OE2" Residue "E GLU 752": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30407 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.81, per 1000 atoms: 0.49 Number of scatterers: 30407 At special positions: 0 Unit cell: (176.79, 157.7, 181.77, 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 107 16.00 P 6 15.00 O 5769 8.00 N 5345 7.00 C 19180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.50 Conformation dependent library (CDL) restraints added in 5.4 seconds 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 141 helices and 25 sheets defined 40.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.25 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 146 through 150 removed outlier: 4.278A pdb=" N LEU A 149 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 150 " --> pdb=" O TYR A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 150' Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 236 removed outlier: 3.758A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.755A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.121A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 495 through 512 removed outlier: 5.576A pdb=" N TRP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 680 through 691 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 737 through 745 removed outlier: 4.002A pdb=" N GLU A 744 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 762 through 768 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 118 through 138 removed outlier: 3.646A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 185 through 236 Processing helix chain 'B' and resid 239 through 255 removed outlier: 6.153A pdb=" N LEU B 246 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 248 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 255 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 435 through 443 removed outlier: 3.592A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 507 through 514 Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 631 through 647 removed outlier: 3.503A pdb=" N TYR B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 691 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 737 through 743 removed outlier: 4.424A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 743 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 120 through 136 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 147 through 154 removed outlier: 4.185A pdb=" N VAL C 152 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS C 153 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 154 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 167 removed outlier: 3.948A pdb=" N ASP C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 185 through 241 Processing helix chain 'C' and resid 246 through 253 Processing helix chain 'C' and resid 260 through 271 Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 326 through 337 Processing helix chain 'C' and resid 362 through 371 Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 447 through 450 Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 495 through 504 removed outlier: 3.892A pdb=" N GLN C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 513 Processing helix chain 'C' and resid 525 through 533 removed outlier: 3.812A pdb=" N ARG C 529 " --> pdb=" O ALA C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 557 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 631 through 646 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 658 through 660 No H-bonds generated for 'chain 'C' and resid 658 through 660' Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 740 through 743 No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 748 through 753 Processing helix chain 'C' and resid 763 through 773 removed outlier: 3.683A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 771 " --> pdb=" O GLU C 767 " (cutoff:3.500A) Proline residue: C 772 - end of helix Processing helix chain 'D' and resid 31 through 38 Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.716A pdb=" N ALA D 151 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 152 " --> pdb=" O LEU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 185 through 237 Processing helix chain 'D' and resid 240 through 255 removed outlier: 4.535A pdb=" N LEU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.693A pdb=" N VAL D 285 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA D 286 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D 295 " --> pdb=" O TRP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'D' and resid 324 through 337 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 435 through 443 removed outlier: 3.573A pdb=" N VAL D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 495 through 505 Processing helix chain 'D' and resid 507 through 514 Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'D' and resid 541 through 559 Processing helix chain 'D' and resid 574 through 578 Processing helix chain 'D' and resid 631 through 646 removed outlier: 3.913A pdb=" N GLU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 651 Processing helix chain 'D' and resid 658 through 660 No H-bonds generated for 'chain 'D' and resid 658 through 660' Processing helix chain 'D' and resid 677 through 692 removed outlier: 4.721A pdb=" N ILE D 681 " --> pdb=" O SER D 678 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER D 692 " --> pdb=" O SER D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 741 through 744 No H-bonds generated for 'chain 'D' and resid 741 through 744' Processing helix chain 'D' and resid 751 through 753 No H-bonds generated for 'chain 'D' and resid 751 through 753' Processing helix chain 'D' and resid 762 through 768 Processing helix chain 'E' and resid 31 through 38 Processing helix chain 'E' and resid 118 through 138 Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 186 through 233 Processing helix chain 'E' and resid 246 through 252 removed outlier: 3.638A pdb=" N ARG E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 272 removed outlier: 3.840A pdb=" N LYS E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 291 removed outlier: 3.732A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.793A pdb=" N ARG E 336 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 371 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 424 through 426 No H-bonds generated for 'chain 'E' and resid 424 through 426' Processing helix chain 'E' and resid 435 through 442 removed outlier: 3.551A pdb=" N LEU E 440 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 442 " --> pdb=" O MET E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 481 No H-bonds generated for 'chain 'E' and resid 479 through 481' Processing helix chain 'E' and resid 495 through 512 removed outlier: 3.735A pdb=" N TYR E 505 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRP E 507 " --> pdb=" O ARG E 503 " (cutoff:3.500A) Proline residue: E 508 - end of helix Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 542 through 560 removed outlier: 3.532A pdb=" N GLU E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 577 No H-bonds generated for 'chain 'E' and resid 574 through 577' Processing helix chain 'E' and resid 631 through 646 Processing helix chain 'E' and resid 657 through 660 Processing helix chain 'E' and resid 680 through 691 Processing helix chain 'E' and resid 718 through 728 Processing helix chain 'E' and resid 740 through 744 Processing helix chain 'E' and resid 748 through 751 No H-bonds generated for 'chain 'E' and resid 748 through 751' Processing helix chain 'E' and resid 762 through 768 Processing sheet with id= A, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.836A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 520 through 522 removed outlier: 7.093A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 596 through 600 Processing sheet with id= D, first strand: chain 'A' and resid 615 through 618 Processing sheet with id= E, first strand: chain 'A' and resid 733 through 736 Processing sheet with id= F, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.746A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 86 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 25 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 85 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 73 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU B 87 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL B 71 " --> pdb=" O GLU B 87 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.837A pdb=" N ASP B 96 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG B 104 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 378 through 380 removed outlier: 7.630A pdb=" N LEU B 420 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 468 " --> pdb=" O LEU B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.444A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 43 through 45 Processing sheet with id= K, first strand: chain 'C' and resid 350 through 354 Processing sheet with id= L, first strand: chain 'C' and resid 418 through 420 removed outlier: 6.569A pdb=" N PHE C 466 " --> pdb=" O ILE C 419 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.157A pdb=" N LYS C 732 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU C 755 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU C 735 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS C 757 " --> pdb=" O LEU C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.568A pdb=" N LEU D 3 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU D 5 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA D 105 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 7 through 9 removed outlier: 6.141A pdb=" N PHE D 45 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 73 through 75 removed outlier: 3.730A pdb=" N GLN D 73 " --> pdb=" O MET D 85 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET D 75 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN D 83 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 353 through 355 removed outlier: 6.145A pdb=" N ILE D 488 " --> pdb=" O VAL D 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 378 through 380 removed outlier: 6.939A pdb=" N LEU D 420 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE D 468 " --> pdb=" O LEU D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 613 through 615 removed outlier: 4.186A pdb=" N GLU D 613 " --> pdb=" O HIS D 666 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D 666 " --> pdb=" O GLU D 613 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 615 " --> pdb=" O HIS D 664 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS D 664 " --> pdb=" O ALA D 615 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.164A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= V, first strand: chain 'E' and resid 20 through 22 removed outlier: 3.644A pdb=" N GLU E 87 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN E 68 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG E 91 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY E 66 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 350 through 354 Processing sheet with id= X, first strand: chain 'E' and resid 418 through 421 removed outlier: 7.256A pdb=" N PHE E 466 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU E 421 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE E 468 " --> pdb=" O LEU E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 613 through 617 1018 hydrogen bonds defined for protein. 2871 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: 10.39 Time building geometry restraints manager: 12.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 10321 1.35 - 1.50: 7745 1.50 - 1.65: 12673 1.65 - 1.80: 135 1.80 - 1.94: 77 Bond restraints: 30951 Sorted by residual: bond pdb=" C THR B 603 " pdb=" N PRO B 604 " ideal model delta sigma weight residual 1.333 1.385 -0.052 1.44e-02 4.82e+03 1.32e+01 bond pdb=" N THR A 603 " pdb=" CA THR A 603 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.29e+01 bond pdb=" N VAL B 352 " pdb=" CA VAL B 352 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.08e-02 8.57e+03 1.11e+01 bond pdb=" N ALA B 348 " pdb=" CA ALA B 348 " ideal model delta sigma weight residual 1.456 1.484 -0.028 8.70e-03 1.32e+04 1.05e+01 bond pdb=" N ILE B 468 " pdb=" CA ILE B 468 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.02e+01 ... (remaining 30946 not shown) Histogram of bond angle deviations from ideal: 95.24 - 103.45: 477 103.45 - 111.66: 13338 111.66 - 119.87: 14519 119.87 - 128.08: 13361 128.08 - 136.29: 259 Bond angle restraints: 41954 Sorted by residual: angle pdb=" C ASP E 324 " pdb=" N VAL E 325 " pdb=" CA VAL E 325 " ideal model delta sigma weight residual 121.97 132.69 -10.72 1.80e+00 3.09e-01 3.55e+01 angle pdb=" C ARG B 345 " pdb=" N ASN B 346 " pdb=" CA ASN B 346 " ideal model delta sigma weight residual 121.90 114.49 7.41 1.26e+00 6.30e-01 3.46e+01 angle pdb=" N GLU B 228 " pdb=" CA GLU B 228 " pdb=" CB GLU B 228 " ideal model delta sigma weight residual 110.39 120.04 -9.65 1.66e+00 3.63e-01 3.38e+01 angle pdb=" CA GLU B 423 " pdb=" CB GLU B 423 " pdb=" CG GLU B 423 " ideal model delta sigma weight residual 114.10 125.34 -11.24 2.00e+00 2.50e-01 3.16e+01 angle pdb=" C HIS D 319 " pdb=" N TYR D 320 " pdb=" CA TYR D 320 " ideal model delta sigma weight residual 121.19 129.82 -8.63 1.59e+00 3.96e-01 2.94e+01 ... (remaining 41949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.79: 18548 29.79 - 59.58: 530 59.58 - 89.36: 55 89.36 - 119.15: 1 119.15 - 148.94: 1 Dihedral angle restraints: 19135 sinusoidal: 7985 harmonic: 11150 Sorted by residual: dihedral pdb=" CA ILE C 390 " pdb=" C ILE C 390 " pdb=" N ARG C 391 " pdb=" CA ARG C 391 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA MET D 698 " pdb=" C MET D 698 " pdb=" N ASP D 699 " pdb=" CA ASP D 699 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU B 771 " pdb=" C LEU B 771 " pdb=" N PRO B 772 " pdb=" CA PRO B 772 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 19132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4349 0.117 - 0.234: 397 0.234 - 0.351: 32 0.351 - 0.468: 3 0.468 - 0.585: 1 Chirality restraints: 4782 Sorted by residual: chirality pdb=" CB ILE C 490 " pdb=" CA ILE C 490 " pdb=" CG1 ILE C 490 " pdb=" CG2 ILE C 490 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" CB ILE D 308 " pdb=" CA ILE D 308 " pdb=" CG1 ILE D 308 " pdb=" CG2 ILE D 308 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB VAL A 718 " pdb=" CA VAL A 718 " pdb=" CG1 VAL A 718 " pdb=" CG2 VAL A 718 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 4779 not shown) Planarity restraints: 5457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 298 " 0.038 2.00e-02 2.50e+03 2.94e-02 2.16e+01 pdb=" CG TRP A 298 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A 298 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 298 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 298 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 298 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 298 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 298 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 298 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 298 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 225 " 0.018 2.00e-02 2.50e+03 2.49e-02 1.24e+01 pdb=" CG TYR A 225 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 225 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 225 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR A 225 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 225 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 225 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 225 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 203 " 0.029 2.00e-02 2.50e+03 2.64e-02 1.22e+01 pdb=" CG PHE A 203 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 203 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 203 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 203 " 0.000 2.00e-02 2.50e+03 ... (remaining 5454 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2898 2.74 - 3.28: 31352 3.28 - 3.82: 55867 3.82 - 4.36: 66269 4.36 - 4.90: 103935 Nonbonded interactions: 260321 Sorted by model distance: nonbonded pdb=" OG1 THR E 682 " pdb=" O MET E 702 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR B 648 " pdb=" O PRO B 654 " model vdw 2.208 2.440 nonbonded pdb=" O1A AGS D 801 " pdb=" O2B AGS D 801 " model vdw 2.210 2.440 nonbonded pdb=" O1A AGS B 801 " pdb=" O2G AGS B 801 " model vdw 2.218 2.440 nonbonded pdb=" O THR D 685 " pdb=" OG SER D 689 " model vdw 2.219 2.440 ... (remaining 260316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 774) selection = chain 'C' selection = (chain 'D' and resid 2 through 774) selection = chain 'E' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.240 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: 0.030 Extract box with map and model: 13.780 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 75.980 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 30951 Z= 0.515 Angle : 1.310 15.480 41954 Z= 0.708 Chirality : 0.071 0.585 4782 Planarity : 0.009 0.081 5457 Dihedral : 14.043 148.938 11955 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.46 % Favored : 91.49 % Rotamer: Outliers : 0.15 % Allowed : 0.77 % Favored : 99.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.12), residues: 3855 helix: -2.00 (0.11), residues: 1578 sheet: -2.52 (0.25), residues: 358 loop : -2.51 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP A 298 HIS 0.023 0.003 HIS B 726 PHE 0.060 0.003 PHE A 203 TYR 0.061 0.003 TYR A 225 ARG 0.028 0.001 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 244 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8627 (t0) cc_final: 0.8378 (t0) REVERT: A 226 LEU cc_start: 0.8952 (mt) cc_final: 0.8650 (pp) REVERT: A 401 MET cc_start: 0.8930 (tpp) cc_final: 0.8473 (mmm) REVERT: B 230 MET cc_start: 0.6645 (ppp) cc_final: 0.6287 (ppp) REVERT: B 258 MET cc_start: 0.1242 (mtt) cc_final: 0.0438 (mtt) REVERT: B 496 MET cc_start: 0.9233 (tmm) cc_final: 0.8842 (tmm) REVERT: B 633 MET cc_start: 0.8277 (mpp) cc_final: 0.7972 (mpp) REVERT: B 635 GLU cc_start: 0.8799 (tp30) cc_final: 0.8476 (mm-30) REVERT: C 68 GLN cc_start: 0.8323 (tp40) cc_final: 0.7787 (tp40) REVERT: C 217 MET cc_start: 0.9511 (mmp) cc_final: 0.9310 (mmm) REVERT: C 230 MET cc_start: 0.8532 (ppp) cc_final: 0.8297 (ppp) REVERT: D 258 MET cc_start: 0.4258 (mmm) cc_final: 0.3912 (mmm) REVERT: E 85 MET cc_start: 0.7744 (tpt) cc_final: 0.7329 (tpp) REVERT: E 217 MET cc_start: 0.9016 (mmt) cc_final: 0.8397 (tmm) outliers start: 5 outliers final: 1 residues processed: 248 average time/residue: 0.4720 time to fit residues: 188.9393 Evaluate side-chains 188 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 3.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 50.0000 chunk 291 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 349 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 GLN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN D 221 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 HIS E 638 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 30951 Z= 0.360 Angle : 0.822 11.987 41954 Z= 0.422 Chirality : 0.048 0.240 4782 Planarity : 0.006 0.064 5457 Dihedral : 7.881 150.747 4292 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 31.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.27 % Favored : 91.70 % Rotamer: Outliers : 0.86 % Allowed : 8.32 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -2.80 (0.13), residues: 3855 helix: -1.17 (0.12), residues: 1591 sheet: -2.78 (0.24), residues: 377 loop : -2.25 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 292 HIS 0.009 0.002 HIS C 666 PHE 0.023 0.002 PHE C 466 TYR 0.030 0.002 TYR D 643 ARG 0.011 0.001 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8489 (t0) cc_final: 0.8172 (t0) REVERT: B 230 MET cc_start: 0.6591 (ppp) cc_final: 0.6122 (ppp) REVERT: B 258 MET cc_start: 0.2415 (mtt) cc_final: 0.1669 (mtt) REVERT: C 68 GLN cc_start: 0.8494 (tp40) cc_final: 0.7996 (tp-100) REVERT: C 230 MET cc_start: 0.8406 (ppp) cc_final: 0.8175 (ppp) REVERT: C 276 MET cc_start: 0.8767 (tpp) cc_final: 0.8467 (tpp) REVERT: D 258 MET cc_start: 0.4653 (mmm) cc_final: 0.4200 (mmt) REVERT: D 336 ARG cc_start: 0.8404 (mmp80) cc_final: 0.8105 (mmm160) REVERT: D 372 MET cc_start: 0.8586 (tmm) cc_final: 0.8361 (tmm) REVERT: E 85 MET cc_start: 0.7811 (tpt) cc_final: 0.7312 (tpp) REVERT: E 217 MET cc_start: 0.9010 (mmt) cc_final: 0.8414 (tmm) REVERT: E 427 MET cc_start: 0.3065 (tpt) cc_final: 0.2665 (mmm) REVERT: E 485 MET cc_start: 0.8994 (mpp) cc_final: 0.8295 (mpp) outliers start: 28 outliers final: 18 residues processed: 202 average time/residue: 0.4262 time to fit residues: 138.0886 Evaluate side-chains 187 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 309 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 238 optimal weight: 0.0170 chunk 96 optimal weight: 50.0000 chunk 350 optimal weight: 40.0000 chunk 378 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 347 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 280 optimal weight: 2.9990 overall best weight: 1.4224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30951 Z= 0.195 Angle : 0.682 11.708 41954 Z= 0.341 Chirality : 0.045 0.205 4782 Planarity : 0.005 0.057 5457 Dihedral : 7.444 150.458 4290 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.58 % Rotamer: Outliers : 1.08 % Allowed : 10.97 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -2.39 (0.13), residues: 3855 helix: -0.74 (0.12), residues: 1609 sheet: -2.51 (0.24), residues: 365 loop : -2.13 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 563 HIS 0.007 0.001 HIS C 666 PHE 0.015 0.001 PHE C 657 TYR 0.019 0.001 TYR B 332 ARG 0.008 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8452 (t0) cc_final: 0.8107 (t0) REVERT: A 226 LEU cc_start: 0.8994 (mt) cc_final: 0.8598 (pp) REVERT: B 230 MET cc_start: 0.6590 (ppp) cc_final: 0.6061 (ppp) REVERT: B 258 MET cc_start: 0.1699 (mtt) cc_final: 0.0693 (mpp) REVERT: B 293 LEU cc_start: 0.8941 (tt) cc_final: 0.8062 (mt) REVERT: B 372 MET cc_start: 0.6529 (tpt) cc_final: 0.6203 (tpt) REVERT: B 439 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8787 (tmm) REVERT: B 516 MET cc_start: 0.6785 (tmm) cc_final: 0.6532 (tmm) REVERT: C 68 GLN cc_start: 0.8296 (tp40) cc_final: 0.7821 (tp-100) REVERT: C 230 MET cc_start: 0.8325 (ppp) cc_final: 0.8043 (ppp) REVERT: C 339 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7242 (p) REVERT: C 423 GLU cc_start: 0.7906 (tp30) cc_final: 0.7601 (tp30) REVERT: C 439 MET cc_start: 0.8706 (tpp) cc_final: 0.8457 (tpp) REVERT: D 258 MET cc_start: 0.4457 (mmm) cc_final: 0.4156 (mmt) REVERT: D 485 MET cc_start: 0.7769 (ppp) cc_final: 0.7102 (ppp) REVERT: E 85 MET cc_start: 0.7832 (tpt) cc_final: 0.7342 (tpp) outliers start: 35 outliers final: 19 residues processed: 221 average time/residue: 0.4212 time to fit residues: 150.9599 Evaluate side-chains 199 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 0.0050 chunk 263 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 351 optimal weight: 20.0000 chunk 372 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 chunk 333 optimal weight: 0.0870 chunk 100 optimal weight: 20.0000 overall best weight: 3.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30951 Z= 0.251 Angle : 0.697 10.966 41954 Z= 0.347 Chirality : 0.045 0.220 4782 Planarity : 0.005 0.052 5457 Dihedral : 7.305 148.994 4290 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 27.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.17 % Favored : 91.80 % Rotamer: Outliers : 1.57 % Allowed : 14.08 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -2.17 (0.13), residues: 3855 helix: -0.50 (0.13), residues: 1602 sheet: -2.37 (0.25), residues: 356 loop : -2.09 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 563 HIS 0.006 0.001 HIS C 666 PHE 0.016 0.001 PHE C 466 TYR 0.026 0.002 TYR D 643 ARG 0.016 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 185 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8557 (t0) cc_final: 0.8216 (t0) REVERT: A 226 LEU cc_start: 0.9102 (mt) cc_final: 0.8736 (pp) REVERT: A 546 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: B 230 MET cc_start: 0.6351 (ppp) cc_final: 0.5800 (ppp) REVERT: B 258 MET cc_start: 0.2123 (mtt) cc_final: 0.1527 (mtt) REVERT: B 372 MET cc_start: 0.6812 (tpt) cc_final: 0.6177 (tpt) REVERT: B 516 MET cc_start: 0.6910 (tmm) cc_final: 0.6584 (tmm) REVERT: C 68 GLN cc_start: 0.8321 (tp40) cc_final: 0.7888 (tp40) REVERT: C 85 MET cc_start: 0.6699 (tpp) cc_final: 0.6365 (tpp) REVERT: C 230 MET cc_start: 0.8341 (ppp) cc_final: 0.8068 (ppp) REVERT: C 423 GLU cc_start: 0.7986 (tp30) cc_final: 0.7604 (tp30) REVERT: C 439 MET cc_start: 0.8783 (tpp) cc_final: 0.8579 (tpp) REVERT: D 258 MET cc_start: 0.4424 (mmm) cc_final: 0.4069 (mmt) REVERT: D 372 MET cc_start: 0.8618 (tmm) cc_final: 0.8002 (tmm) REVERT: E 85 MET cc_start: 0.7877 (tpt) cc_final: 0.7372 (tpp) REVERT: E 217 MET cc_start: 0.9256 (mmp) cc_final: 0.8633 (ppp) REVERT: E 221 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8965 (pp30) REVERT: E 683 MET cc_start: -0.3069 (mmt) cc_final: -0.3943 (mtt) outliers start: 51 outliers final: 33 residues processed: 221 average time/residue: 0.4163 time to fit residues: 150.4110 Evaluate side-chains 210 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 50.0000 chunk 211 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 317 optimal weight: 0.0570 chunk 257 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 190 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30951 Z= 0.252 Angle : 0.691 12.179 41954 Z= 0.343 Chirality : 0.044 0.224 4782 Planarity : 0.005 0.053 5457 Dihedral : 7.253 149.566 4290 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 28.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.38 % Favored : 91.60 % Rotamer: Outliers : 2.13 % Allowed : 15.13 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -2.09 (0.13), residues: 3855 helix: -0.38 (0.13), residues: 1593 sheet: -2.43 (0.25), residues: 370 loop : -2.05 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 563 HIS 0.005 0.001 HIS C 666 PHE 0.017 0.001 PHE C 657 TYR 0.026 0.002 TYR D 643 ARG 0.011 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 181 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8598 (t0) cc_final: 0.8257 (t0) REVERT: A 226 LEU cc_start: 0.9176 (mt) cc_final: 0.8894 (pp) REVERT: A 258 MET cc_start: 0.3719 (tpt) cc_final: 0.3042 (mmm) REVERT: A 546 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: A 623 LEU cc_start: 0.8545 (tp) cc_final: 0.8155 (pp) REVERT: A 666 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8628 (t70) REVERT: B 230 MET cc_start: 0.6214 (ppp) cc_final: 0.5681 (ppp) REVERT: B 258 MET cc_start: 0.2039 (mtt) cc_final: 0.1498 (mtt) REVERT: B 372 MET cc_start: 0.6851 (tpt) cc_final: 0.6185 (tpt) REVERT: B 516 MET cc_start: 0.6917 (tmm) cc_final: 0.6553 (tmm) REVERT: B 626 THR cc_start: 0.7651 (p) cc_final: 0.7371 (p) REVERT: C 68 GLN cc_start: 0.8266 (tp40) cc_final: 0.7888 (tp40) REVERT: C 85 MET cc_start: 0.6681 (tpp) cc_final: 0.6346 (tpp) REVERT: C 230 MET cc_start: 0.8315 (ppp) cc_final: 0.8002 (ppp) REVERT: C 262 VAL cc_start: 0.2220 (OUTLIER) cc_final: 0.1777 (t) REVERT: C 276 MET cc_start: 0.8857 (tpp) cc_final: 0.8442 (tpp) REVERT: C 423 GLU cc_start: 0.7985 (tp30) cc_final: 0.7577 (tp30) REVERT: C 439 MET cc_start: 0.8804 (tpp) cc_final: 0.8581 (tpp) REVERT: C 552 ARG cc_start: 0.7302 (mpt180) cc_final: 0.6819 (tpt170) REVERT: D 258 MET cc_start: 0.4447 (mmm) cc_final: 0.4045 (mmt) REVERT: D 372 MET cc_start: 0.8549 (tmm) cc_final: 0.8188 (tmm) REVERT: E 85 MET cc_start: 0.7905 (tpt) cc_final: 0.7380 (tpp) REVERT: E 485 MET cc_start: 0.9003 (mpp) cc_final: 0.8216 (mpp) outliers start: 69 outliers final: 47 residues processed: 236 average time/residue: 0.4125 time to fit residues: 159.4908 Evaluate side-chains 225 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 372 optimal weight: 30.0000 chunk 309 optimal weight: 40.0000 chunk 172 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 30951 Z= 0.272 Angle : 0.720 21.615 41954 Z= 0.354 Chirality : 0.045 0.237 4782 Planarity : 0.005 0.059 5457 Dihedral : 7.269 148.884 4290 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 29.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 2.59 % Allowed : 16.02 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -2.04 (0.13), residues: 3855 helix: -0.33 (0.13), residues: 1595 sheet: -2.44 (0.25), residues: 369 loop : -2.03 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 563 HIS 0.005 0.001 HIS C 666 PHE 0.017 0.001 PHE C 466 TYR 0.026 0.002 TYR D 643 ARG 0.011 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 177 time to evaluate : 3.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8649 (t0) cc_final: 0.8312 (t0) REVERT: A 226 LEU cc_start: 0.9269 (mt) cc_final: 0.8961 (pp) REVERT: A 258 MET cc_start: 0.4002 (tpt) cc_final: 0.3333 (mmm) REVERT: A 546 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: A 623 LEU cc_start: 0.8621 (tp) cc_final: 0.8212 (pp) REVERT: B 230 MET cc_start: 0.6229 (ppp) cc_final: 0.5662 (ppp) REVERT: B 258 MET cc_start: 0.2374 (mtt) cc_final: 0.1854 (mtt) REVERT: B 516 MET cc_start: 0.7050 (tmm) cc_final: 0.6324 (tmm) REVERT: C 68 GLN cc_start: 0.8262 (tp40) cc_final: 0.7875 (tp40) REVERT: C 85 MET cc_start: 0.6868 (tpp) cc_final: 0.6526 (tpp) REVERT: C 230 MET cc_start: 0.8312 (ppp) cc_final: 0.8003 (ppp) REVERT: C 262 VAL cc_start: 0.2250 (OUTLIER) cc_final: 0.1775 (t) REVERT: C 423 GLU cc_start: 0.8042 (tp30) cc_final: 0.7655 (tp30) REVERT: C 439 MET cc_start: 0.8856 (tpp) cc_final: 0.8614 (tpp) REVERT: D 258 MET cc_start: 0.4555 (mmm) cc_final: 0.4147 (mmt) REVERT: D 344 VAL cc_start: 0.1611 (OUTLIER) cc_final: 0.1344 (t) REVERT: D 427 MET cc_start: 0.6046 (tmm) cc_final: 0.5513 (tmm) REVERT: D 486 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: E 85 MET cc_start: 0.7938 (tpt) cc_final: 0.7399 (tpp) outliers start: 84 outliers final: 58 residues processed: 245 average time/residue: 0.4122 time to fit residues: 165.4812 Evaluate side-chains 236 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 174 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 738 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 633 MET Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 272 optimal weight: 0.0670 chunk 210 optimal weight: 9.9990 chunk 313 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 371 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 171 optimal weight: 40.0000 overall best weight: 2.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30951 Z= 0.226 Angle : 0.695 18.976 41954 Z= 0.340 Chirality : 0.044 0.244 4782 Planarity : 0.005 0.049 5457 Dihedral : 7.194 149.137 4290 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 27.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.19 % Allowed : 17.26 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -1.93 (0.13), residues: 3855 helix: -0.25 (0.13), residues: 1593 sheet: -2.38 (0.26), residues: 363 loop : -1.96 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 563 HIS 0.005 0.001 HIS D 319 PHE 0.021 0.001 PHE C 657 TYR 0.021 0.001 TYR D 643 ARG 0.009 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 193 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8673 (t0) cc_final: 0.8344 (t0) REVERT: A 226 LEU cc_start: 0.9223 (mt) cc_final: 0.8922 (pp) REVERT: A 258 MET cc_start: 0.4039 (tpt) cc_final: 0.3363 (mmm) REVERT: A 546 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: A 623 LEU cc_start: 0.8588 (tp) cc_final: 0.8186 (pp) REVERT: B 230 MET cc_start: 0.6263 (ppp) cc_final: 0.5690 (ppp) REVERT: B 258 MET cc_start: 0.2108 (mtt) cc_final: 0.1632 (mtt) REVERT: B 372 MET cc_start: 0.6902 (tpt) cc_final: 0.6494 (tpt) REVERT: B 439 MET cc_start: 0.8669 (tmm) cc_final: 0.8072 (ppp) REVERT: B 516 MET cc_start: 0.6973 (tmm) cc_final: 0.6161 (tmm) REVERT: B 626 THR cc_start: 0.7610 (p) cc_final: 0.7315 (p) REVERT: C 68 GLN cc_start: 0.8189 (tp40) cc_final: 0.7822 (tp40) REVERT: C 85 MET cc_start: 0.6888 (tpp) cc_final: 0.6561 (tpp) REVERT: C 230 MET cc_start: 0.8352 (ppp) cc_final: 0.8030 (ppp) REVERT: C 262 VAL cc_start: 0.2312 (OUTLIER) cc_final: 0.1829 (t) REVERT: C 423 GLU cc_start: 0.8080 (tp30) cc_final: 0.7701 (tp30) REVERT: C 439 MET cc_start: 0.8828 (tpp) cc_final: 0.8568 (tpp) REVERT: C 552 ARG cc_start: 0.7316 (mpt180) cc_final: 0.6822 (tpt170) REVERT: C 702 MET cc_start: 0.6327 (mpp) cc_final: 0.5186 (mmt) REVERT: D 258 MET cc_start: 0.4435 (mmm) cc_final: 0.3901 (mmt) REVERT: D 344 VAL cc_start: 0.1555 (OUTLIER) cc_final: 0.1295 (t) REVERT: D 372 MET cc_start: 0.8492 (tmm) cc_final: 0.8274 (tmm) REVERT: D 427 MET cc_start: 0.6061 (tmm) cc_final: 0.5512 (tmm) REVERT: D 486 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: E 85 MET cc_start: 0.7933 (tpt) cc_final: 0.7390 (tpp) outliers start: 71 outliers final: 54 residues processed: 250 average time/residue: 0.4082 time to fit residues: 168.6128 Evaluate side-chains 234 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 176 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 738 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30951 Z= 0.211 Angle : 0.683 16.799 41954 Z= 0.334 Chirality : 0.044 0.236 4782 Planarity : 0.005 0.048 5457 Dihedral : 7.124 149.437 4290 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 26.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.37 % Allowed : 17.47 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -1.84 (0.14), residues: 3855 helix: -0.18 (0.13), residues: 1601 sheet: -2.30 (0.26), residues: 363 loop : -1.91 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 563 HIS 0.005 0.001 HIS B 407 PHE 0.016 0.001 PHE C 466 TYR 0.020 0.001 TYR D 643 ARG 0.008 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 186 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8651 (t0) cc_final: 0.8305 (t0) REVERT: A 226 LEU cc_start: 0.9209 (mt) cc_final: 0.8886 (pp) REVERT: A 258 MET cc_start: 0.4006 (tpt) cc_final: 0.3412 (mmm) REVERT: A 372 MET cc_start: 0.8184 (ptt) cc_final: 0.7717 (ppp) REVERT: A 546 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: A 623 LEU cc_start: 0.8609 (tp) cc_final: 0.8195 (pp) REVERT: B 230 MET cc_start: 0.6098 (ppp) cc_final: 0.5122 (ppp) REVERT: B 372 MET cc_start: 0.6890 (tpt) cc_final: 0.6387 (tpt) REVERT: B 439 MET cc_start: 0.8576 (tmm) cc_final: 0.8053 (ppp) REVERT: B 626 THR cc_start: 0.7583 (p) cc_final: 0.7308 (p) REVERT: C 68 GLN cc_start: 0.8139 (tp40) cc_final: 0.7775 (tp40) REVERT: C 85 MET cc_start: 0.6863 (tpp) cc_final: 0.6537 (tpp) REVERT: C 230 MET cc_start: 0.8342 (ppp) cc_final: 0.8029 (ppp) REVERT: C 262 VAL cc_start: 0.2472 (OUTLIER) cc_final: 0.1980 (t) REVERT: C 423 GLU cc_start: 0.8070 (tp30) cc_final: 0.7673 (tp30) REVERT: C 439 MET cc_start: 0.8812 (tpp) cc_final: 0.8554 (tpp) REVERT: D 258 MET cc_start: 0.4248 (mmm) cc_final: 0.3668 (mmt) REVERT: D 344 VAL cc_start: 0.1250 (OUTLIER) cc_final: 0.0980 (t) REVERT: D 427 MET cc_start: 0.6018 (tmm) cc_final: 0.5476 (tmm) REVERT: D 486 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: D 524 ASP cc_start: 0.9301 (m-30) cc_final: 0.8681 (t0) REVERT: E 85 MET cc_start: 0.7940 (tpt) cc_final: 0.7407 (tpp) outliers start: 77 outliers final: 60 residues processed: 248 average time/residue: 0.3998 time to fit residues: 163.0298 Evaluate side-chains 243 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 179 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 768 TYR Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 738 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 687 ILE Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 0.9980 chunk 355 optimal weight: 30.0000 chunk 324 optimal weight: 50.0000 chunk 345 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 271 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 327 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30951 Z= 0.233 Angle : 0.706 15.692 41954 Z= 0.343 Chirality : 0.044 0.291 4782 Planarity : 0.005 0.058 5457 Dihedral : 7.099 149.636 4290 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.16 % Allowed : 17.94 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -1.82 (0.14), residues: 3855 helix: -0.16 (0.13), residues: 1605 sheet: -2.19 (0.26), residues: 367 loop : -1.94 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 563 HIS 0.006 0.001 HIS E 168 PHE 0.022 0.001 PHE C 657 TYR 0.023 0.001 TYR D 643 ARG 0.008 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 184 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8659 (t0) cc_final: 0.8312 (t0) REVERT: A 258 MET cc_start: 0.4143 (tpt) cc_final: 0.3517 (mmm) REVERT: A 372 MET cc_start: 0.8276 (ptt) cc_final: 0.7749 (ppp) REVERT: A 546 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: A 623 LEU cc_start: 0.8661 (tp) cc_final: 0.8204 (pp) REVERT: B 230 MET cc_start: 0.5706 (ppp) cc_final: 0.5304 (ppp) REVERT: B 439 MET cc_start: 0.8528 (tmm) cc_final: 0.8029 (ppp) REVERT: B 626 THR cc_start: 0.7594 (p) cc_final: 0.7314 (p) REVERT: C 68 GLN cc_start: 0.8128 (tp40) cc_final: 0.7744 (tp40) REVERT: C 85 MET cc_start: 0.6889 (tpp) cc_final: 0.6565 (tpp) REVERT: C 230 MET cc_start: 0.8332 (ppp) cc_final: 0.8018 (ppp) REVERT: C 262 VAL cc_start: 0.2569 (OUTLIER) cc_final: 0.2076 (t) REVERT: C 339 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7103 (p) REVERT: C 423 GLU cc_start: 0.8059 (tp30) cc_final: 0.7650 (tp30) REVERT: C 439 MET cc_start: 0.8831 (tpp) cc_final: 0.8567 (tpp) REVERT: C 702 MET cc_start: 0.6644 (mpp) cc_final: 0.5357 (mmt) REVERT: D 258 MET cc_start: 0.4349 (mmm) cc_final: 0.3699 (mmt) REVERT: D 344 VAL cc_start: 0.1405 (OUTLIER) cc_final: 0.1113 (t) REVERT: D 486 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: E 85 MET cc_start: 0.7956 (tpt) cc_final: 0.7411 (tpp) outliers start: 70 outliers final: 60 residues processed: 241 average time/residue: 0.4096 time to fit residues: 160.9919 Evaluate side-chains 248 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 183 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 738 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.8980 chunk 365 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 173 optimal weight: 50.0000 chunk 254 optimal weight: 9.9990 chunk 383 optimal weight: 6.9990 chunk 353 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30951 Z= 0.226 Angle : 0.708 15.161 41954 Z= 0.344 Chirality : 0.045 0.280 4782 Planarity : 0.005 0.049 5457 Dihedral : 7.072 150.006 4290 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.10 % Allowed : 18.18 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -1.80 (0.14), residues: 3855 helix: -0.16 (0.13), residues: 1605 sheet: -2.16 (0.26), residues: 364 loop : -1.92 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 563 HIS 0.006 0.001 HIS E 18 PHE 0.016 0.001 PHE C 466 TYR 0.021 0.001 TYR D 643 ARG 0.007 0.000 ARG C 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 185 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8672 (t0) cc_final: 0.8339 (t0) REVERT: A 226 LEU cc_start: 0.9168 (mt) cc_final: 0.8798 (pp) REVERT: A 258 MET cc_start: 0.4161 (tpt) cc_final: 0.3574 (mmm) REVERT: A 372 MET cc_start: 0.8273 (ptt) cc_final: 0.7730 (ppp) REVERT: A 516 MET cc_start: 0.7362 (ppp) cc_final: 0.6171 (ppp) REVERT: A 546 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: B 230 MET cc_start: 0.5585 (ppp) cc_final: 0.5195 (ppp) REVERT: B 372 MET cc_start: 0.6826 (tpt) cc_final: 0.6431 (tpt) REVERT: B 439 MET cc_start: 0.8504 (tmm) cc_final: 0.8015 (ppp) REVERT: B 626 THR cc_start: 0.7561 (p) cc_final: 0.7285 (p) REVERT: C 68 GLN cc_start: 0.8101 (tp40) cc_final: 0.7715 (tp40) REVERT: C 85 MET cc_start: 0.6905 (tpp) cc_final: 0.6578 (tpp) REVERT: C 230 MET cc_start: 0.8308 (ppp) cc_final: 0.7989 (ppp) REVERT: C 262 VAL cc_start: 0.2927 (OUTLIER) cc_final: 0.2442 (t) REVERT: C 339 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6992 (p) REVERT: C 423 GLU cc_start: 0.8043 (tp30) cc_final: 0.7632 (tp30) REVERT: C 439 MET cc_start: 0.8819 (tpp) cc_final: 0.8557 (tpp) REVERT: C 702 MET cc_start: 0.6639 (mpp) cc_final: 0.5289 (mmt) REVERT: D 258 MET cc_start: 0.4263 (mmm) cc_final: 0.3622 (mmt) REVERT: D 344 VAL cc_start: 0.1357 (OUTLIER) cc_final: 0.1069 (t) REVERT: D 372 MET cc_start: 0.8567 (tmm) cc_final: 0.7933 (tmm) REVERT: D 486 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: D 524 ASP cc_start: 0.9373 (m-30) cc_final: 0.9002 (p0) REVERT: E 85 MET cc_start: 0.7990 (tpt) cc_final: 0.7493 (tpp) REVERT: E 217 MET cc_start: 0.9049 (mmt) cc_final: 0.8333 (ppp) outliers start: 68 outliers final: 60 residues processed: 241 average time/residue: 0.4241 time to fit residues: 167.4882 Evaluate side-chains 244 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 179 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 748 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 738 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 719 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 30.0000 chunk 325 optimal weight: 7.9990 chunk 93 optimal weight: 30.0000 chunk 281 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 0.0870 chunk 305 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 314 optimal weight: 50.0000 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.123174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.076445 restraints weight = 103244.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.076460 restraints weight = 110580.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.076202 restraints weight = 110347.605| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30951 Z= 0.257 Angle : 0.728 14.593 41954 Z= 0.354 Chirality : 0.045 0.287 4782 Planarity : 0.005 0.053 5457 Dihedral : 7.098 149.757 4290 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 30.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.25 % Allowed : 18.37 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % 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: -1.81 (0.14), residues: 3855 helix: -0.15 (0.13), residues: 1597 sheet: -2.12 (0.27), residues: 358 loop : -1.96 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 563 HIS 0.006 0.001 HIS E 18 PHE 0.021 0.001 PHE C 657 TYR 0.026 0.002 TYR D 643 ARG 0.010 0.000 ARG B 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5926.53 seconds wall clock time: 111 minutes 30.14 seconds (6690.14 seconds total)