Starting phenix.real_space_refine on Tue Jul 23 02:03:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/07_2024/7n5d_24186.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/07_2024/7n5d_24186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/07_2024/7n5d_24186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/07_2024/7n5d_24186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/07_2024/7n5d_24186.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/07_2024/7n5d_24186.cif" } resolution = 2.8 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= 0.002 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 13516 2.51 5 N 3419 2.21 5 O 3574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 625": "OE1" <-> "OE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 746": "OE1" <-> "OE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 611": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 695": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20593 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 378} Chain breaks: 5 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.09, per 1000 atoms: 0.54 Number of scatterers: 20593 At special positions: 0 Unit cell: (147.29, 144.2, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3574 8.00 N 3419 7.00 C 13516 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: 8.33 Conformation dependent library (CDL) restraints added in 4.0 seconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5066 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 9 sheets defined 64.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.855A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 259 through 283 removed outlier: 5.237A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 333 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 504 through 552 Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 661 through 678 Processing helix chain 'A' and resid 714 through 737 Processing helix chain 'B' and resid 187 through 203 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 265 through 285 Processing helix chain 'B' and resid 295 through 329 removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 331 No H-bonds generated for 'chain 'B' and resid 330 through 331' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 590 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 661 through 678 Processing helix chain 'B' and resid 714 through 737 Processing helix chain 'C' and resid 187 through 203 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 235 through 242 Processing helix chain 'C' and resid 265 through 285 Processing helix chain 'C' and resid 295 through 329 removed outlier: 3.892A pdb=" N SER C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 331 No H-bonds generated for 'chain 'C' and resid 330 through 331' Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 352 removed outlier: 3.519A pdb=" N GLN C 350 " --> pdb=" O HIS C 346 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 524 Processing helix chain 'C' and resid 526 through 552 Processing helix chain 'C' and resid 556 through 590 removed outlier: 5.551A pdb=" N ASN C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 661 through 678 Processing helix chain 'C' and resid 714 through 737 Processing helix chain 'D' and resid 187 through 203 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 235 through 242 Processing helix chain 'D' and resid 265 through 285 Processing helix chain 'D' and resid 295 through 327 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 352 removed outlier: 3.541A pdb=" N GLN D 350 " --> pdb=" O HIS D 346 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 524 Processing helix chain 'D' and resid 526 through 552 Processing helix chain 'D' and resid 556 through 590 removed outlier: 5.586A pdb=" N ASN D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 635 Processing helix chain 'D' and resid 661 through 678 Processing helix chain 'D' and resid 714 through 737 Processing helix chain 'E' and resid 187 through 203 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 235 through 242 Processing helix chain 'E' and resid 265 through 285 Processing helix chain 'E' and resid 295 through 327 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 352 removed outlier: 3.661A pdb=" N GLN E 350 " --> pdb=" O HIS E 346 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR E 351 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 524 Processing helix chain 'E' and resid 526 through 552 Processing helix chain 'E' and resid 556 through 590 removed outlier: 5.669A pdb=" N ASN E 576 " --> pdb=" O PHE E 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 635 Processing helix chain 'E' and resid 661 through 678 Processing helix chain 'E' and resid 714 through 736 Processing helix chain 'F' and resid 187 through 203 Processing helix chain 'F' and resid 223 through 232 removed outlier: 3.722A pdb=" N GLY F 232 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 241 Processing helix chain 'F' and resid 265 through 285 Processing helix chain 'F' and resid 295 through 329 removed outlier: 3.985A pdb=" N SER F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 331 No H-bonds generated for 'chain 'F' and resid 330 through 331' Processing helix chain 'F' and resid 332 through 334 No H-bonds generated for 'chain 'F' and resid 332 through 334' Processing helix chain 'F' and resid 335 through 352 Processing helix chain 'F' and resid 508 through 524 Processing helix chain 'F' and resid 526 through 552 Processing helix chain 'F' and resid 556 through 590 removed outlier: 5.688A pdb=" N ASN F 576 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 661 through 678 Processing helix chain 'F' and resid 714 through 737 Processing helix chain 'G' and resid 187 through 203 Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 235 through 242 Processing helix chain 'G' and resid 265 through 285 Processing helix chain 'G' and resid 295 through 329 removed outlier: 3.906A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 331 No H-bonds generated for 'chain 'G' and resid 330 through 331' Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 352 Processing helix chain 'G' and resid 508 through 524 Processing helix chain 'G' and resid 526 through 552 Processing helix chain 'G' and resid 556 through 590 removed outlier: 5.688A pdb=" N ASN G 576 " --> pdb=" O PHE G 572 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 635 Processing helix chain 'G' and resid 661 through 678 Processing helix chain 'G' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 626 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 626 " --> pdb=" O ASN C 641 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 618 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N MET C 612 " --> pdb=" O THR C 616 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR C 616 " --> pdb=" O MET C 612 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 626 " --> pdb=" O ASN D 641 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 618 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N MET D 612 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS D 626 " --> pdb=" O ASN E 641 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL E 618 " --> pdb=" O GLU E 610 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET E 612 " --> pdb=" O THR E 616 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR E 616 " --> pdb=" O MET E 612 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS E 626 " --> pdb=" O ASN F 641 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 618 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS F 626 " --> pdb=" O ASN G 641 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL G 618 " --> pdb=" O GLU G 610 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET G 612 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR G 616 " --> pdb=" O MET G 612 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS G 626 " --> pdb=" O ASN A 641 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.531A pdb=" N LYS A 699 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 694 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS A 701 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 707 " --> pdb=" O GLN A 686 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 686 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 745 through 750 removed outlier: 6.485A pdb=" N GLN A 745 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG B 750 " --> pdb=" O GLN A 745 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE A 747 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE G 749 " --> pdb=" O ARG A 750 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.484A pdb=" N LYS B 699 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 694 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 701 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 649 through 657 removed outlier: 6.416A pdb=" N LYS C 699 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE C 694 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS C 701 " --> pdb=" O LYS C 692 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 707 " --> pdb=" O GLN C 686 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN C 686 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 649 through 657 removed outlier: 6.507A pdb=" N LYS D 699 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE D 694 " --> pdb=" O LYS D 699 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS D 701 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 649 through 657 removed outlier: 6.465A pdb=" N LYS E 699 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE E 694 " --> pdb=" O LYS E 699 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS E 701 " --> pdb=" O LYS E 692 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 649 through 657 removed outlier: 6.506A pdb=" N LYS F 699 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE F 694 " --> pdb=" O LYS F 699 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS F 701 " --> pdb=" O LYS F 692 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN F 707 " --> pdb=" O GLN F 686 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN F 686 " --> pdb=" O ASN F 707 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 649 through 657 removed outlier: 6.330A pdb=" N LYS G 699 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE G 694 " --> pdb=" O LYS G 699 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS G 701 " --> pdb=" O LYS G 692 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN G 707 " --> pdb=" O GLN G 686 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN G 686 " --> pdb=" O ASN G 707 " (cutoff:3.500A) 1505 hydrogen bonds defined for protein. 4437 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: 6.50 Time building geometry restraints manager: 9.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3829 1.31 - 1.44: 5375 1.44 - 1.56: 11510 1.56 - 1.69: 113 1.69 - 1.82: 147 Bond restraints: 20974 Sorted by residual: bond pdb=" CB ILE E 285 " pdb=" CG1 ILE E 285 " ideal model delta sigma weight residual 1.530 1.672 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" CB ILE F 285 " pdb=" CG1 ILE F 285 " ideal model delta sigma weight residual 1.530 1.671 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" CB ILE G 285 " pdb=" CG1 ILE G 285 " ideal model delta sigma weight residual 1.530 1.667 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.47e+01 bond pdb=" CD2 TRP D 507 " pdb=" CE3 TRP D 507 " ideal model delta sigma weight residual 1.398 1.505 -0.107 1.60e-02 3.91e+03 4.46e+01 ... (remaining 20969 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.71: 335 105.71 - 112.90: 11316 112.90 - 120.09: 8686 120.09 - 127.27: 7847 127.27 - 134.46: 240 Bond angle restraints: 28424 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.08 -8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" C GLN G 291 " pdb=" N PRO G 292 " pdb=" CA PRO G 292 " ideal model delta sigma weight residual 119.47 128.27 -8.80 1.16e+00 7.43e-01 5.76e+01 angle pdb=" C GLN C 291 " pdb=" N PRO C 292 " pdb=" CA PRO C 292 " ideal model delta sigma weight residual 119.56 127.00 -7.44 1.02e+00 9.61e-01 5.32e+01 angle pdb=" N THR C 557 " pdb=" CA THR C 557 " pdb=" C THR C 557 " ideal model delta sigma weight residual 112.89 121.73 -8.84 1.24e+00 6.50e-01 5.08e+01 angle pdb=" C HIS E 592 " pdb=" N PRO E 593 " pdb=" CA PRO E 593 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.01e+00 9.80e-01 5.02e+01 ... (remaining 28419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 12108 17.71 - 35.42: 257 35.42 - 53.13: 50 53.13 - 70.84: 30 70.84 - 88.54: 12 Dihedral angle restraints: 12457 sinusoidal: 4779 harmonic: 7678 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.54 88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2784 0.110 - 0.220: 601 0.220 - 0.330: 46 0.330 - 0.440: 9 0.440 - 0.550: 12 Chirality restraints: 3452 Sorted by residual: chirality pdb=" CG LEU C 264 " pdb=" CB LEU C 264 " pdb=" CD1 LEU C 264 " pdb=" CD2 LEU C 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.14 0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -3.12 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 3449 not shown) Planarity restraints: 3469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 291 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLN E 291 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN E 291 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO E 292 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 675 " 0.044 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR E 675 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR E 675 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 675 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 675 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 675 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 675 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 675 " 0.042 2.00e-02 2.50e+03 ... (remaining 3466 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 7757 2.88 - 3.39: 21201 3.39 - 3.89: 34646 3.89 - 4.40: 39809 4.40 - 4.90: 62906 Nonbonded interactions: 166319 Sorted by model distance: nonbonded pdb=" OD1 ASP F 737 " pdb=" NZ LYS F 739 " model vdw 2.378 2.520 nonbonded pdb=" OD1 ASP G 737 " pdb=" NZ LYS G 739 " model vdw 2.385 2.520 nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 2.520 nonbonded pdb=" OD1 ASP D 737 " pdb=" NZ LYS D 739 " model vdw 2.399 2.520 nonbonded pdb=" OD1 ASP E 737 " pdb=" NZ LYS E 739 " model vdw 2.399 2.520 ... (remaining 166314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 186 through 203 or resid 222 through 242 or resid 264 thro \ ugh 354 or resid 507 through 751 or resid 801)) selection = (chain 'B' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'C' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'D' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'E' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'F' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'G' and (resid 186 through 285 or resid 294 through 751 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 54.590 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.023 0.142 20974 Z= 1.464 Angle : 1.521 8.842 28424 Z= 1.044 Chirality : 0.093 0.550 3452 Planarity : 0.008 0.043 3469 Dihedral : 9.909 88.544 7391 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.15), residues: 2540 helix: 1.53 (0.11), residues: 1580 sheet: 0.56 (0.31), residues: 290 loop : 1.05 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.008 TRP E 683 HIS 0.010 0.002 HIS A 331 PHE 0.059 0.005 PHE A 335 TYR 0.044 0.008 TYR E 675 ARG 0.006 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 794 time to evaluate : 2.109 Fit side-chains REVERT: A 311 ILE cc_start: 0.8728 (mt) cc_final: 0.8502 (mm) REVERT: A 325 ILE cc_start: 0.8581 (mt) cc_final: 0.8294 (mt) REVERT: A 525 ASN cc_start: 0.7725 (t0) cc_final: 0.7345 (t0) REVERT: B 300 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7184 (mp0) REVERT: B 526 LYS cc_start: 0.8486 (mttt) cc_final: 0.7916 (mtpp) REVERT: C 304 TRP cc_start: 0.8104 (m100) cc_final: 0.7693 (m100) REVERT: C 525 ASN cc_start: 0.7029 (t0) cc_final: 0.5993 (t0) REVERT: C 526 LYS cc_start: 0.7602 (mttt) cc_final: 0.7398 (mmmm) REVERT: C 595 ASP cc_start: 0.7585 (m-30) cc_final: 0.7253 (m-30) REVERT: D 314 PHE cc_start: 0.8224 (t80) cc_final: 0.7703 (t80) REVERT: D 329 SER cc_start: 0.8520 (m) cc_final: 0.7877 (p) REVERT: D 526 LYS cc_start: 0.8635 (mttt) cc_final: 0.8422 (mmtm) REVERT: D 621 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7421 (mtmt) REVERT: D 625 GLU cc_start: 0.7377 (tt0) cc_final: 0.6938 (tt0) REVERT: F 671 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8246 (mmm-85) REVERT: F 717 GLU cc_start: 0.8625 (tp30) cc_final: 0.8381 (mm-30) REVERT: F 735 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7350 (mt-10) REVERT: G 282 VAL cc_start: 0.7420 (m) cc_final: 0.7153 (p) REVERT: G 526 LYS cc_start: 0.8236 (mttt) cc_final: 0.8028 (mptt) REVERT: G 748 SER cc_start: 0.8856 (t) cc_final: 0.8640 (p) outliers start: 0 outliers final: 6 residues processed: 794 average time/residue: 1.2029 time to fit residues: 1082.9480 Evaluate side-chains 646 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 640 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain G residue 311 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 203 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 515 GLN A 576 ASN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 576 ASN C 648 GLN D 291 GLN D 525 ASN D 576 ASN D 687 HIS D 713 GLN E 533 ASN E 648 GLN E 698 ASN F 345 HIS F 525 ASN F 648 GLN G 533 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20974 Z= 0.250 Angle : 0.592 9.141 28424 Z= 0.310 Chirality : 0.043 0.325 3452 Planarity : 0.004 0.042 3469 Dihedral : 7.080 59.503 2793 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.80 % Allowed : 13.72 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.16), residues: 2540 helix: 2.54 (0.12), residues: 1612 sheet: 0.41 (0.27), residues: 329 loop : 0.71 (0.28), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 273 HIS 0.007 0.001 HIS A 592 PHE 0.021 0.002 PHE D 301 TYR 0.010 0.002 TYR C 629 ARG 0.006 0.001 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 684 time to evaluate : 2.282 Fit side-chains revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7829 (mt-10) REVERT: A 302 VAL cc_start: 0.8575 (t) cc_final: 0.8337 (m) REVERT: A 315 LEU cc_start: 0.8252 (mt) cc_final: 0.8037 (mt) REVERT: A 330 PHE cc_start: 0.7437 (t80) cc_final: 0.7130 (t80) REVERT: A 576 ASN cc_start: 0.7367 (t0) cc_final: 0.7083 (t0) REVERT: B 324 LYS cc_start: 0.8304 (mmtt) cc_final: 0.8098 (mmtt) REVERT: B 583 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 686 GLN cc_start: 0.8035 (mp-120) cc_final: 0.7819 (mp10) REVERT: C 525 ASN cc_start: 0.6893 (t0) cc_final: 0.6513 (t0) REVERT: C 595 ASP cc_start: 0.7567 (m-30) cc_final: 0.7362 (m-30) REVERT: C 713 GLN cc_start: 0.8141 (tp40) cc_final: 0.7882 (tp40) REVERT: D 297 LYS cc_start: 0.7137 (tttt) cc_final: 0.6929 (mmpt) REVERT: D 314 PHE cc_start: 0.7961 (t80) cc_final: 0.7736 (t80) REVERT: D 689 MET cc_start: 0.8363 (ttp) cc_final: 0.8154 (ttp) REVERT: E 739 LYS cc_start: 0.8604 (mttp) cc_final: 0.8279 (mttp) REVERT: F 671 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8204 (mmm-85) REVERT: F 735 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7504 (mt-10) REVERT: G 715 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7455 (m-80) outliers start: 82 outliers final: 31 residues processed: 709 average time/residue: 1.1826 time to fit residues: 957.0242 Evaluate side-chains 685 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 653 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain F residue 547 ILE Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 626 LYS Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 196 optimal weight: 0.0050 chunk 160 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 255 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN A 533 ASN A 686 GLN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN C 698 ASN D 291 GLN D 648 GLN D 698 ASN D 719 ASN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 ASN G 576 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20974 Z= 0.231 Angle : 0.536 8.057 28424 Z= 0.278 Chirality : 0.042 0.245 3452 Planarity : 0.003 0.040 3469 Dihedral : 6.870 59.885 2785 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.17 % Allowed : 17.20 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.17), residues: 2540 helix: 2.71 (0.12), residues: 1613 sheet: 0.49 (0.27), residues: 329 loop : 0.39 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 304 HIS 0.005 0.001 HIS E 708 PHE 0.024 0.002 PHE G 301 TYR 0.012 0.001 TYR E 740 ARG 0.007 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 660 time to evaluate : 2.501 Fit side-chains revert: symmetry clash REVERT: A 300 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 311 ILE cc_start: 0.8748 (tp) cc_final: 0.8486 (tp) REVERT: A 576 ASN cc_start: 0.7391 (t0) cc_final: 0.6982 (t0) REVERT: A 737 ASP cc_start: 0.7811 (t0) cc_final: 0.7582 (t0) REVERT: B 576 ASN cc_start: 0.7283 (m-40) cc_final: 0.7070 (m-40) REVERT: B 583 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 686 GLN cc_start: 0.8062 (mp-120) cc_final: 0.7850 (mp10) REVERT: C 300 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7389 (mp0) REVERT: C 304 TRP cc_start: 0.7808 (m100) cc_final: 0.7418 (m100) REVERT: C 713 GLN cc_start: 0.8101 (tp40) cc_final: 0.7777 (tp40) REVERT: D 282 VAL cc_start: 0.7782 (p) cc_final: 0.7576 (m) REVERT: D 297 LYS cc_start: 0.7220 (tttt) cc_final: 0.7016 (mmpt) REVERT: D 664 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8032 (tptm) REVERT: E 318 VAL cc_start: 0.9067 (t) cc_final: 0.8867 (p) REVERT: E 325 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8549 (pp) REVERT: E 739 LYS cc_start: 0.8543 (mttp) cc_final: 0.8278 (mttp) REVERT: F 548 TRP cc_start: 0.8248 (t60) cc_final: 0.7762 (t60) REVERT: F 671 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8211 (mmm-85) REVERT: F 735 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7397 (mt-10) REVERT: G 545 ILE cc_start: 0.8716 (mp) cc_final: 0.8493 (mp) outliers start: 90 outliers final: 48 residues processed: 686 average time/residue: 1.2045 time to fit residues: 945.2564 Evaluate side-chains 689 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 639 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 569 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 543 MET Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 559 LEU Chi-restraints excluded: chain G residue 565 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 122 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 251 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 686 GLN B 686 GLN C 576 ASN C 648 GLN C 698 ASN D 291 GLN D 531 GLN D 576 ASN E 531 GLN E 688 ASN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 ASN F 688 ASN G 576 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20974 Z= 0.251 Angle : 0.540 11.356 28424 Z= 0.275 Chirality : 0.042 0.300 3452 Planarity : 0.003 0.037 3469 Dihedral : 6.667 57.602 2783 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.36 % Allowed : 17.94 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.17), residues: 2540 helix: 2.77 (0.12), residues: 1613 sheet: 0.55 (0.27), residues: 329 loop : 0.21 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 304 HIS 0.007 0.001 HIS E 708 PHE 0.022 0.002 PHE D 301 TYR 0.010 0.001 TYR E 740 ARG 0.003 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 644 time to evaluate : 2.490 Fit side-chains revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7127 (pmt170) cc_final: 0.6887 (pmt170) REVERT: A 300 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 576 ASN cc_start: 0.7448 (t0) cc_final: 0.7106 (t0) REVERT: A 737 ASP cc_start: 0.7860 (t0) cc_final: 0.7320 (t0) REVERT: A 739 LYS cc_start: 0.8252 (ptpp) cc_final: 0.8029 (pttm) REVERT: B 583 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 686 GLN cc_start: 0.8073 (mp10) cc_final: 0.7869 (mp10) REVERT: C 300 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 304 TRP cc_start: 0.7888 (m100) cc_final: 0.7522 (m100) REVERT: C 713 GLN cc_start: 0.8075 (tp40) cc_final: 0.7828 (tp40) REVERT: E 325 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8572 (pp) REVERT: F 548 TRP cc_start: 0.8240 (t60) cc_final: 0.7934 (t60) REVERT: G 545 ILE cc_start: 0.8698 (mp) cc_final: 0.8464 (mp) REVERT: G 715 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7522 (m-80) outliers start: 94 outliers final: 51 residues processed: 675 average time/residue: 1.2148 time to fit residues: 931.6299 Evaluate side-chains 687 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 634 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 543 MET Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 693 GLU Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 317 LEU Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 626 LYS Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 3 optimal weight: 0.0170 chunk 187 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS A 513 ASN A 533 ASN A 605 ASN A 686 GLN C 576 ASN C 648 GLN D 291 GLN D 531 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 576 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20974 Z= 0.162 Angle : 0.507 10.010 28424 Z= 0.257 Chirality : 0.041 0.198 3452 Planarity : 0.003 0.035 3469 Dihedral : 6.378 58.047 2783 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.89 % Allowed : 19.10 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.17), residues: 2540 helix: 2.94 (0.12), residues: 1613 sheet: 0.56 (0.27), residues: 319 loop : 0.14 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 273 HIS 0.004 0.001 HIS E 708 PHE 0.025 0.001 PHE F 301 TYR 0.007 0.001 TYR E 740 ARG 0.004 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 639 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7020 (pmt170) cc_final: 0.6762 (pmt170) REVERT: A 300 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 323 LEU cc_start: 0.8294 (mt) cc_final: 0.7978 (tm) REVERT: A 737 ASP cc_start: 0.7852 (t0) cc_final: 0.7246 (t0) REVERT: A 739 LYS cc_start: 0.8229 (ptpp) cc_final: 0.7986 (pttm) REVERT: B 689 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: C 300 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7418 (mp0) REVERT: C 713 GLN cc_start: 0.8038 (tp40) cc_final: 0.7813 (tp40) REVERT: E 300 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7515 (mp0) REVERT: E 325 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8555 (pp) REVERT: E 648 GLN cc_start: 0.8409 (mt0) cc_final: 0.8171 (mt0) REVERT: F 671 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8130 (mmm-85) REVERT: G 545 ILE cc_start: 0.8675 (mp) cc_final: 0.8458 (mp) outliers start: 84 outliers final: 41 residues processed: 666 average time/residue: 1.1770 time to fit residues: 892.5312 Evaluate side-chains 668 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 625 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 543 MET Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 739 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 208 optimal weight: 0.0570 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 686 GLN C 525 ASN C 576 ASN C 648 GLN D 291 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN E 688 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN F 696 ASN G 576 ASN G 681 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20974 Z= 0.193 Angle : 0.506 8.624 28424 Z= 0.257 Chirality : 0.041 0.191 3452 Planarity : 0.003 0.034 3469 Dihedral : 6.223 58.691 2781 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.71 % Allowed : 19.80 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.17), residues: 2540 helix: 2.99 (0.12), residues: 1614 sheet: 0.55 (0.27), residues: 329 loop : 0.11 (0.28), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 548 HIS 0.004 0.001 HIS A 592 PHE 0.028 0.001 PHE G 301 TYR 0.012 0.001 TYR D 740 ARG 0.003 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 632 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6993 (pmt170) cc_final: 0.6748 (pmt170) REVERT: A 300 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 323 LEU cc_start: 0.8289 (mt) cc_final: 0.7986 (tm) REVERT: A 576 ASN cc_start: 0.7435 (t0) cc_final: 0.7038 (t0) REVERT: A 737 ASP cc_start: 0.7863 (t0) cc_final: 0.7213 (t0) REVERT: A 739 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7994 (pttm) REVERT: B 629 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7881 (t80) REVERT: B 689 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8044 (ttp) REVERT: C 300 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7416 (mp0) REVERT: C 713 GLN cc_start: 0.8009 (tp40) cc_final: 0.7805 (tp40) REVERT: E 300 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 325 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8561 (pp) REVERT: F 671 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8170 (mmm-85) REVERT: G 715 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7431 (m-80) outliers start: 80 outliers final: 51 residues processed: 659 average time/residue: 1.1768 time to fit residues: 880.6750 Evaluate side-chains 674 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 619 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain F residue 739 LYS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 317 LEU Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 250 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN A 686 GLN C 525 ASN ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 576 ASN G 681 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20974 Z= 0.205 Angle : 0.520 9.559 28424 Z= 0.263 Chirality : 0.041 0.194 3452 Planarity : 0.003 0.035 3469 Dihedral : 6.170 58.556 2781 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.89 % Allowed : 19.89 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.17), residues: 2540 helix: 3.00 (0.12), residues: 1614 sheet: 0.52 (0.27), residues: 329 loop : 0.08 (0.28), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 548 HIS 0.005 0.001 HIS E 708 PHE 0.025 0.001 PHE F 301 TYR 0.010 0.001 TYR D 740 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 639 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6967 (pmt170) cc_final: 0.6718 (pmt170) REVERT: A 300 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 323 LEU cc_start: 0.8273 (mt) cc_final: 0.7969 (tm) REVERT: A 576 ASN cc_start: 0.7469 (t0) cc_final: 0.7069 (t0) REVERT: A 737 ASP cc_start: 0.7878 (t0) cc_final: 0.7221 (t0) REVERT: A 739 LYS cc_start: 0.8271 (ptpp) cc_final: 0.8022 (pttm) REVERT: B 629 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7885 (t80) REVERT: B 689 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8043 (ttp) REVERT: C 300 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7452 (mp0) REVERT: C 689 MET cc_start: 0.8381 (ttp) cc_final: 0.8044 (ttp) REVERT: C 713 GLN cc_start: 0.7994 (tp40) cc_final: 0.7793 (tp40) REVERT: E 300 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7497 (mt-10) REVERT: E 325 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8577 (pp) REVERT: F 671 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8220 (mmm-85) outliers start: 84 outliers final: 56 residues processed: 666 average time/residue: 1.1859 time to fit residues: 897.3427 Evaluate side-chains 687 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 628 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 579 LYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 547 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain F residue 739 LYS Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 0.1980 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.0050 chunk 159 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN A 686 GLN C 525 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 576 ASN G 681 ASN G 698 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20974 Z= 0.311 Angle : 0.584 11.010 28424 Z= 0.295 Chirality : 0.043 0.199 3452 Planarity : 0.003 0.035 3469 Dihedral : 6.264 59.489 2781 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.94 % Allowed : 20.63 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.17), residues: 2540 helix: 2.86 (0.12), residues: 1614 sheet: 0.51 (0.27), residues: 329 loop : 0.04 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 548 HIS 0.007 0.001 HIS E 708 PHE 0.029 0.002 PHE G 301 TYR 0.012 0.002 TYR G 740 ARG 0.004 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 635 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7084 (pmt170) cc_final: 0.6846 (pmt170) REVERT: A 300 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7878 (mt-10) REVERT: A 323 LEU cc_start: 0.8299 (mt) cc_final: 0.7993 (tm) REVERT: A 576 ASN cc_start: 0.7528 (t0) cc_final: 0.7086 (t0) REVERT: A 737 ASP cc_start: 0.7901 (t0) cc_final: 0.7287 (t0) REVERT: A 739 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8154 (pttm) REVERT: B 629 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7901 (t80) REVERT: B 689 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8055 (ttp) REVERT: C 300 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7278 (mp0) REVERT: C 689 MET cc_start: 0.8454 (ttp) cc_final: 0.8227 (ttp) REVERT: C 713 GLN cc_start: 0.7988 (tp40) cc_final: 0.7719 (tp40) REVERT: E 300 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 325 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8599 (pp) REVERT: F 671 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8270 (mmm-85) REVERT: G 531 GLN cc_start: 0.7828 (mt0) cc_final: 0.7536 (mt0) REVERT: G 715 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7637 (m-80) outliers start: 85 outliers final: 56 residues processed: 661 average time/residue: 1.2020 time to fit residues: 903.3134 Evaluate side-chains 686 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 626 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 635 CYS Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain F residue 748 SER Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 317 LEU Chi-restraints excluded: chain G residue 549 LEU Chi-restraints excluded: chain G residue 680 LEU Chi-restraints excluded: chain G residue 697 VAL Chi-restraints excluded: chain G residue 715 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 140 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN A 686 GLN C 525 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN G 698 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20974 Z= 0.193 Angle : 0.554 10.795 28424 Z= 0.278 Chirality : 0.041 0.210 3452 Planarity : 0.003 0.033 3469 Dihedral : 6.135 58.671 2781 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.29 % Allowed : 21.37 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.17), residues: 2540 helix: 2.97 (0.12), residues: 1614 sheet: 0.47 (0.27), residues: 329 loop : 0.02 (0.28), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 548 HIS 0.005 0.001 HIS E 708 PHE 0.027 0.001 PHE F 301 TYR 0.008 0.001 TYR D 740 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 618 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.7049 (pmt170) cc_final: 0.6809 (pmt170) REVERT: A 300 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7864 (mt-10) REVERT: A 323 LEU cc_start: 0.8272 (mt) cc_final: 0.7978 (tm) REVERT: A 576 ASN cc_start: 0.7501 (t0) cc_final: 0.7075 (t0) REVERT: A 737 ASP cc_start: 0.7876 (t0) cc_final: 0.7258 (t0) REVERT: A 739 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8130 (pttm) REVERT: B 549 LEU cc_start: 0.8734 (mm) cc_final: 0.8530 (mt) REVERT: B 567 LEU cc_start: 0.8376 (tm) cc_final: 0.8146 (tt) REVERT: B 629 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7920 (t80) REVERT: B 689 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8038 (ttp) REVERT: C 550 ILE cc_start: 0.8817 (mp) cc_final: 0.8596 (tp) REVERT: C 689 MET cc_start: 0.8392 (ttp) cc_final: 0.8134 (ttp) REVERT: C 713 GLN cc_start: 0.7990 (tp40) cc_final: 0.7754 (tp40) REVERT: E 300 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7476 (mt-10) REVERT: E 325 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8600 (pp) REVERT: F 671 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8137 (mmm-85) outliers start: 71 outliers final: 55 residues processed: 642 average time/residue: 1.1938 time to fit residues: 870.7342 Evaluate side-chains 678 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 620 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 545 ILE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 543 MET Chi-restraints excluded: chain F residue 545 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 317 LEU Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.9990 chunk 246 optimal weight: 0.4980 chunk 150 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 171 optimal weight: 0.0000 chunk 259 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 686 GLN C 525 ASN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 696 ASN G 576 ASN G 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20974 Z= 0.188 Angle : 0.576 13.366 28424 Z= 0.286 Chirality : 0.041 0.210 3452 Planarity : 0.003 0.033 3469 Dihedral : 6.078 58.525 2781 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.92 % Allowed : 21.93 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.17), residues: 2540 helix: 2.98 (0.12), residues: 1614 sheet: 0.44 (0.27), residues: 329 loop : 0.03 (0.28), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.030 0.001 PHE G 301 TYR 0.011 0.001 TYR D 740 ARG 0.002 0.000 ARG A 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 612 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ARG cc_start: 0.6955 (pmt170) cc_final: 0.6733 (pmt170) REVERT: A 300 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7847 (mt-10) REVERT: A 323 LEU cc_start: 0.8264 (mt) cc_final: 0.7968 (tm) REVERT: A 576 ASN cc_start: 0.7522 (t0) cc_final: 0.7124 (t0) REVERT: A 737 ASP cc_start: 0.7853 (t0) cc_final: 0.7339 (t0) REVERT: A 739 LYS cc_start: 0.8364 (ptpp) cc_final: 0.8124 (pttm) REVERT: B 567 LEU cc_start: 0.8349 (tm) cc_final: 0.8118 (tt) REVERT: B 629 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7878 (t80) REVERT: B 689 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8039 (ttp) REVERT: C 300 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7328 (mp0) REVERT: C 550 ILE cc_start: 0.8804 (mp) cc_final: 0.8542 (tp) REVERT: C 689 MET cc_start: 0.8382 (ttp) cc_final: 0.8094 (ttp) REVERT: C 713 GLN cc_start: 0.7963 (tp40) cc_final: 0.7728 (tp40) REVERT: E 300 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7483 (mt-10) REVERT: E 325 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8619 (pp) REVERT: F 671 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8127 (mmm-85) outliers start: 63 outliers final: 51 residues processed: 635 average time/residue: 1.2306 time to fit residues: 896.6043 Evaluate side-chains 666 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 612 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 629 TYR Chi-restraints excluded: chain C residue 718 LYS Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 545 ILE Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 541 ILE Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 624 LYS Chi-restraints excluded: chain F residue 678 GLN Chi-restraints excluded: chain F residue 701 LYS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 317 LEU Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 212 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 686 GLN C 525 ASN C 576 ASN D 291 GLN E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN G 681 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109585 restraints weight = 32944.885| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.98 r_work: 0.3312 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20974 Z= 0.182 Angle : 0.583 13.081 28424 Z= 0.289 Chirality : 0.042 0.325 3452 Planarity : 0.003 0.033 3469 Dihedral : 5.987 58.235 2781 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.01 % Allowed : 22.11 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.17), residues: 2540 helix: 3.02 (0.12), residues: 1613 sheet: 0.42 (0.27), residues: 329 loop : 0.06 (0.28), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 548 HIS 0.004 0.001 HIS E 708 PHE 0.027 0.001 PHE F 301 TYR 0.012 0.001 TYR D 740 ARG 0.004 0.000 ARG A 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12280.79 seconds wall clock time: 212 minutes 55.45 seconds (12775.45 seconds total)