Starting phenix.real_space_refine on Mon Mar 18 20:29:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wac_32381/03_2024/7wac_32381.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wac_32381/03_2024/7wac_32381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wac_32381/03_2024/7wac_32381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wac_32381/03_2024/7wac_32381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wac_32381/03_2024/7wac_32381.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wac_32381/03_2024/7wac_32381.pdb" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 72 5.16 5 C 13920 2.51 5 N 3844 2.21 5 O 4180 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 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "B PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "C PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 575": "OE1" <-> "OE2" Residue "D PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "C" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Time building chain proxies: 11.59, per 1000 atoms: 0.53 Number of scatterers: 22016 At special positions: 0 Unit cell: (145.2, 141.68, 104.72, 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 72 16.00 O 4180 8.00 N 3844 7.00 C 13920 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: 8.53 Conformation dependent library (CDL) restraints added in 4.1 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 24 sheets defined 42.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.881A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 3.804A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.697A pdb=" N GLN A 198 " --> pdb=" O GLY A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.421A pdb=" N ASP A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.733A pdb=" N ALA A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.934A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 4.198A pdb=" N GLY A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.564A pdb=" N ALA A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 498 through 513 removed outlier: 3.529A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.515A pdb=" N ALA A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.513A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 608 removed outlier: 3.832A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 690 through 707 removed outlier: 4.099A pdb=" N ILE A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 76 through 91 removed outlier: 3.882A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 3.805A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.696A pdb=" N GLN B 198 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 219 through 230 Processing helix chain 'B' and resid 244 through 254 removed outlier: 4.422A pdb=" N ASP B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.735A pdb=" N ALA B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.933A pdb=" N GLU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 4.198A pdb=" N GLY B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 424 Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.564A pdb=" N ALA B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 498 through 513 removed outlier: 3.530A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.515A pdb=" N ALA B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.514A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 removed outlier: 3.832A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 644 through 653 Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 690 through 707 removed outlier: 4.099A pdb=" N ILE B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 695 " --> pdb=" O PRO B 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 696 " --> pdb=" O PHE B 692 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'C' and resid 43 through 51 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 65 through 74 Processing helix chain 'C' and resid 76 through 91 removed outlier: 3.882A pdb=" N VAL C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.804A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.697A pdb=" N GLN C 198 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 219 through 230 Processing helix chain 'C' and resid 244 through 254 removed outlier: 4.420A pdb=" N ASP C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.734A pdb=" N ALA C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 removed outlier: 4.932A pdb=" N GLU C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 345 " --> pdb=" O GLU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 4.198A pdb=" N GLY C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 424 Processing helix chain 'C' and resid 457 through 462 removed outlier: 3.564A pdb=" N ALA C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 498 through 513 removed outlier: 3.529A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 548 removed outlier: 3.515A pdb=" N ALA C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 567 removed outlier: 3.513A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.832A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 627 through 629 No H-bonds generated for 'chain 'C' and resid 627 through 629' Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 682 through 686 Processing helix chain 'C' and resid 690 through 707 removed outlier: 4.100A pdb=" N ILE C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 695 " --> pdb=" O PRO C 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 696 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 76 through 91 removed outlier: 3.882A pdb=" N VAL D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 140 removed outlier: 3.805A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.697A pdb=" N GLN D 198 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 244 through 254 removed outlier: 4.422A pdb=" N ASP D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.734A pdb=" N ALA D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 4.933A pdb=" N GLU D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 345 " --> pdb=" O GLU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 374 removed outlier: 4.198A pdb=" N GLY D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 424 Processing helix chain 'D' and resid 457 through 462 removed outlier: 3.564A pdb=" N ALA D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 498 through 513 removed outlier: 3.530A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 548 removed outlier: 3.514A pdb=" N ALA D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.514A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 608 removed outlier: 3.831A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 626 Processing helix chain 'D' and resid 627 through 629 No H-bonds generated for 'chain 'D' and resid 627 through 629' Processing helix chain 'D' and resid 644 through 653 Processing helix chain 'D' and resid 682 through 686 Processing helix chain 'D' and resid 690 through 707 removed outlier: 4.099A pdb=" N ILE D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 695 " --> pdb=" O PRO D 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN D 696 " --> pdb=" O PHE D 692 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 6.376A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 5.110A pdb=" N VAL A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 313 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 319 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 429 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 451 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP A 431 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 533 removed outlier: 5.603A pdb=" N LEU A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 527 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 490 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE A 578 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 492 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU A 575 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A 634 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 613 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA A 636 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA A 615 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE A 638 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 617 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 9 removed outlier: 6.376A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 237 through 240 Processing sheet with id=AB1, first strand: chain 'B' and resid 400 through 403 removed outlier: 5.110A pdb=" N VAL B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 313 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 319 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY B 429 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 451 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 431 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AB3, first strand: chain 'B' and resid 530 through 533 removed outlier: 5.604A pdb=" N LEU B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE B 527 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 490 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 578 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER B 492 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU B 575 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B 634 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 613 " --> pdb=" O GLN B 634 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA B 636 " --> pdb=" O GLY B 613 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA B 615 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE B 638 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 617 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 9 removed outlier: 6.376A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AB7, first strand: chain 'C' and resid 400 through 403 removed outlier: 5.110A pdb=" N VAL C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL C 313 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 319 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY C 429 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 451 " --> pdb=" O GLY C 429 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP C 431 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AB9, first strand: chain 'C' and resid 530 through 533 removed outlier: 5.604A pdb=" N LEU C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE C 527 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 490 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE C 578 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER C 492 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU C 575 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN C 634 " --> pdb=" O PRO C 611 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY C 613 " --> pdb=" O GLN C 634 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA C 636 " --> pdb=" O GLY C 613 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA C 615 " --> pdb=" O ALA C 636 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE C 638 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 617 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 2 through 9 removed outlier: 6.375A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'D' and resid 237 through 240 Processing sheet with id=AC4, first strand: chain 'D' and resid 400 through 403 removed outlier: 5.110A pdb=" N VAL D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL D 313 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 319 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY D 429 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL D 451 " --> pdb=" O GLY D 429 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP D 431 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 327 through 328 Processing sheet with id=AC6, first strand: chain 'D' and resid 530 through 533 removed outlier: 5.602A pdb=" N LEU D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE D 527 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE D 490 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE D 578 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER D 492 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLU D 575 " --> pdb=" O LYS D 612 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN D 634 " --> pdb=" O PRO D 611 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY D 613 " --> pdb=" O GLN D 634 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA D 636 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA D 615 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE D 638 " --> pdb=" O ALA D 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 617 " --> pdb=" O PHE D 638 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2868 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: 7.97 Time building geometry restraints manager: 9.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7408 1.34 - 1.46: 3843 1.46 - 1.58: 11005 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 22376 Sorted by residual: bond pdb=" CG1 ILE D 211 " pdb=" CD1 ILE D 211 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CG1 ILE B 211 " pdb=" CD1 ILE B 211 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CG1 ILE C 211 " pdb=" CD1 ILE C 211 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 bond pdb=" CG1 ILE A 211 " pdb=" CD1 ILE A 211 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.40e+00 bond pdb=" CA MET D 627 " pdb=" C MET D 627 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.80e-02 3.09e+03 6.80e-01 ... (remaining 22371 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 573 106.39 - 113.30: 12597 113.30 - 120.20: 7581 120.20 - 127.10: 9393 127.10 - 134.00: 200 Bond angle restraints: 30344 Sorted by residual: angle pdb=" C CYS C 59 " pdb=" N SER C 60 " pdb=" CA SER C 60 " ideal model delta sigma weight residual 120.58 124.20 -3.62 1.32e+00 5.74e-01 7.51e+00 angle pdb=" C CYS D 59 " pdb=" N SER D 60 " pdb=" CA SER D 60 " ideal model delta sigma weight residual 120.58 124.17 -3.59 1.32e+00 5.74e-01 7.41e+00 angle pdb=" C CYS B 59 " pdb=" N SER B 60 " pdb=" CA SER B 60 " ideal model delta sigma weight residual 120.58 124.17 -3.59 1.32e+00 5.74e-01 7.39e+00 angle pdb=" C CYS A 59 " pdb=" N SER A 60 " pdb=" CA SER A 60 " ideal model delta sigma weight residual 120.58 124.16 -3.58 1.32e+00 5.74e-01 7.35e+00 angle pdb=" N THR A 204 " pdb=" CA THR A 204 " pdb=" C THR A 204 " ideal model delta sigma weight residual 114.64 110.84 3.80 1.52e+00 4.33e-01 6.24e+00 ... (remaining 30339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 12367 17.46 - 34.91: 873 34.91 - 52.37: 184 52.37 - 69.82: 20 69.82 - 87.28: 40 Dihedral angle restraints: 13484 sinusoidal: 5300 harmonic: 8184 Sorted by residual: dihedral pdb=" CG ARG C 236 " pdb=" CD ARG C 236 " pdb=" NE ARG C 236 " pdb=" CZ ARG C 236 " ideal model delta sinusoidal sigma weight residual -180.00 -135.64 -44.36 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 236 " pdb=" CD ARG A 236 " pdb=" NE ARG A 236 " pdb=" CZ ARG A 236 " ideal model delta sinusoidal sigma weight residual -180.00 -135.65 -44.35 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG B 236 " pdb=" CD ARG B 236 " pdb=" NE ARG B 236 " pdb=" CZ ARG B 236 " ideal model delta sinusoidal sigma weight residual 180.00 -135.65 -44.35 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 13481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2437 0.036 - 0.073: 743 0.073 - 0.109: 293 0.109 - 0.146: 87 0.146 - 0.182: 8 Chirality restraints: 3568 Sorted by residual: chirality pdb=" CA ILE A 260 " pdb=" N ILE A 260 " pdb=" C ILE A 260 " pdb=" CB ILE A 260 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA ILE C 260 " pdb=" N ILE C 260 " pdb=" C ILE C 260 " pdb=" CB ILE C 260 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 3565 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 60 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A 61 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 60 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO C 61 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 60 " 0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 61 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " 0.023 5.00e-02 4.00e+02 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2794 2.76 - 3.29: 20604 3.29 - 3.83: 35024 3.83 - 4.36: 39433 4.36 - 4.90: 72178 Nonbonded interactions: 170033 Sorted by model distance: nonbonded pdb=" OG1 THR D 335 " pdb=" O ILE D 377 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR A 335 " pdb=" O ILE A 377 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR B 335 " pdb=" O ILE B 377 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR C 335 " pdb=" O ILE C 377 " model vdw 2.221 2.440 nonbonded pdb=" NH1 ARG B 301 " pdb=" O TYR B 302 " model vdw 2.277 2.520 ... (remaining 170028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.080 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 57.630 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.110 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:14.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.002 0.047 22376 Z= 0.163 Angle : 0.511 6.868 30344 Z= 0.285 Chirality : 0.044 0.182 3568 Planarity : 0.003 0.040 3912 Dihedral : 13.361 87.275 8276 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 2884 helix: 1.76 (0.16), residues: 1072 sheet: 0.71 (0.22), residues: 520 loop : -1.03 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 15 HIS 0.003 0.000 HIS A 79 PHE 0.007 0.001 PHE A 243 TYR 0.009 0.001 TYR C 519 ARG 0.002 0.000 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.743 Fit side-chains REVERT: A 160 GLN cc_start: 0.9119 (tt0) cc_final: 0.8723 (tm-30) REVERT: A 300 GLU cc_start: 0.7201 (pm20) cc_final: 0.6958 (pm20) REVERT: B 160 GLN cc_start: 0.9145 (tt0) cc_final: 0.8725 (tm-30) REVERT: C 160 GLN cc_start: 0.9136 (tt0) cc_final: 0.8737 (tm-30) REVERT: D 32 LEU cc_start: 0.8854 (mp) cc_final: 0.8313 (tt) REVERT: D 252 TYR cc_start: 0.8625 (t80) cc_final: 0.8425 (t80) REVERT: D 300 GLU cc_start: 0.7295 (pm20) cc_final: 0.6990 (pm20) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 1.1662 time to fit residues: 213.1636 Evaluate side-chains 111 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 225 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 247 GLN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 247 GLN B 344 ASN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN C 247 GLN C 344 ASN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN D 247 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 22376 Z= 0.423 Angle : 0.564 9.458 30344 Z= 0.301 Chirality : 0.047 0.184 3568 Planarity : 0.004 0.035 3912 Dihedral : 4.156 17.056 3124 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.36 % Allowed : 4.98 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 2884 helix: 1.77 (0.16), residues: 1132 sheet: 0.47 (0.21), residues: 516 loop : -1.10 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 278 HIS 0.004 0.001 HIS D 650 PHE 0.013 0.001 PHE D 43 TYR 0.012 0.001 TYR A 530 ARG 0.008 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 2.477 Fit side-chains REVERT: A 160 GLN cc_start: 0.9062 (tt0) cc_final: 0.8813 (tm-30) REVERT: A 478 MET cc_start: 0.9324 (ttp) cc_final: 0.9113 (ttp) REVERT: B 160 GLN cc_start: 0.9089 (tt0) cc_final: 0.8816 (tm-30) REVERT: C 160 GLN cc_start: 0.9072 (tt0) cc_final: 0.8819 (tm-30) REVERT: D 160 GLN cc_start: 0.9059 (tt0) cc_final: 0.8708 (tm-30) outliers start: 32 outliers final: 18 residues processed: 131 average time/residue: 1.1161 time to fit residues: 173.0881 Evaluate side-chains 121 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 534 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 233 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22376 Z= 0.196 Angle : 0.473 7.915 30344 Z= 0.248 Chirality : 0.044 0.189 3568 Planarity : 0.003 0.033 3912 Dihedral : 3.857 16.519 3124 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.28 % Allowed : 7.45 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 2884 helix: 1.96 (0.16), residues: 1132 sheet: 0.41 (0.21), residues: 516 loop : -1.05 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 278 HIS 0.002 0.000 HIS B 650 PHE 0.010 0.001 PHE B 43 TYR 0.009 0.001 TYR D 519 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.9092 (tt0) cc_final: 0.8840 (tm-30) REVERT: B 160 GLN cc_start: 0.9094 (tt0) cc_final: 0.8797 (tm-30) REVERT: C 160 GLN cc_start: 0.9090 (tt0) cc_final: 0.8839 (tm-30) REVERT: D 58 LEU cc_start: 0.8795 (tt) cc_final: 0.8586 (tm) REVERT: D 138 ASP cc_start: 0.8273 (m-30) cc_final: 0.7515 (t0) REVERT: D 160 GLN cc_start: 0.9087 (tt0) cc_final: 0.8734 (tm-30) outliers start: 30 outliers final: 20 residues processed: 125 average time/residue: 1.1226 time to fit residues: 164.8065 Evaluate side-chains 122 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 40.0000 chunk 125 optimal weight: 5.9990 chunk 175 optimal weight: 0.0170 chunk 262 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22376 Z= 0.264 Angle : 0.490 8.760 30344 Z= 0.256 Chirality : 0.044 0.187 3568 Planarity : 0.003 0.029 3912 Dihedral : 3.859 16.467 3124 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.15 % Allowed : 9.33 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 2884 helix: 1.96 (0.16), residues: 1140 sheet: 0.48 (0.21), residues: 512 loop : -1.11 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 278 HIS 0.002 0.001 HIS D 650 PHE 0.007 0.001 PHE B 43 TYR 0.015 0.001 TYR D 252 ARG 0.004 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.9118 (tt0) cc_final: 0.8853 (tm-30) REVERT: A 612 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8930 (mtpp) REVERT: B 160 GLN cc_start: 0.9107 (tt0) cc_final: 0.8809 (tm-30) REVERT: C 160 GLN cc_start: 0.9110 (tt0) cc_final: 0.8852 (tm-30) REVERT: D 58 LEU cc_start: 0.8770 (tt) cc_final: 0.8551 (tm) REVERT: D 160 GLN cc_start: 0.9100 (tt0) cc_final: 0.8743 (tm-30) outliers start: 27 outliers final: 19 residues processed: 122 average time/residue: 1.2135 time to fit residues: 173.0776 Evaluate side-chains 117 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 252 TYR Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 7.9990 chunk 158 optimal weight: 8.9990 chunk 4 optimal weight: 0.0770 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 249 optimal weight: 40.0000 chunk 70 optimal weight: 0.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22376 Z= 0.121 Angle : 0.440 8.661 30344 Z= 0.231 Chirality : 0.043 0.193 3568 Planarity : 0.003 0.029 3912 Dihedral : 3.605 15.822 3124 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.62 % Allowed : 10.22 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2884 helix: 2.12 (0.16), residues: 1140 sheet: 0.57 (0.21), residues: 508 loop : -1.02 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.002 0.000 HIS A 327 PHE 0.007 0.001 PHE C 638 TYR 0.014 0.001 TYR D 252 ARG 0.005 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.9120 (tt0) cc_final: 0.8845 (tm-30) REVERT: A 612 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8916 (mtpp) REVERT: B 160 GLN cc_start: 0.9116 (tt0) cc_final: 0.8831 (tm-30) REVERT: C 160 GLN cc_start: 0.9111 (tt0) cc_final: 0.8843 (tm-30) REVERT: D 58 LEU cc_start: 0.8675 (tt) cc_final: 0.8450 (tm) REVERT: D 138 ASP cc_start: 0.8291 (m-30) cc_final: 0.7551 (t0) outliers start: 38 outliers final: 17 residues processed: 128 average time/residue: 1.1916 time to fit residues: 178.9911 Evaluate side-chains 114 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 2.9990 chunk 250 optimal weight: 0.0030 chunk 55 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 overall best weight: 3.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22376 Z= 0.196 Angle : 0.465 7.960 30344 Z= 0.245 Chirality : 0.044 0.199 3568 Planarity : 0.003 0.028 3912 Dihedral : 3.625 15.978 3124 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.06 % Allowed : 11.46 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.16), residues: 2884 helix: 2.28 (0.16), residues: 1116 sheet: 0.52 (0.22), residues: 512 loop : -1.03 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 278 HIS 0.002 0.000 HIS D 327 PHE 0.006 0.001 PHE B 43 TYR 0.009 0.001 TYR C 519 ARG 0.005 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.9130 (tt0) cc_final: 0.8860 (tm-30) REVERT: A 612 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8917 (mtpp) REVERT: B 160 GLN cc_start: 0.9130 (tt0) cc_final: 0.8828 (tm-30) REVERT: C 160 GLN cc_start: 0.9124 (tt0) cc_final: 0.8836 (tm-30) REVERT: D 58 LEU cc_start: 0.8674 (tt) cc_final: 0.8465 (tm) outliers start: 25 outliers final: 18 residues processed: 118 average time/residue: 1.1901 time to fit residues: 164.4035 Evaluate side-chains 110 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 158 optimal weight: 30.0000 chunk 203 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22376 Z= 0.278 Angle : 0.490 7.632 30344 Z= 0.260 Chirality : 0.045 0.198 3568 Planarity : 0.003 0.028 3912 Dihedral : 3.783 16.542 3124 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.15 % Allowed : 12.39 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 2884 helix: 2.22 (0.16), residues: 1116 sheet: 0.47 (0.22), residues: 512 loop : -1.03 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 278 HIS 0.002 0.001 HIS D 327 PHE 0.007 0.001 PHE A 480 TYR 0.010 0.001 TYR B 519 ARG 0.005 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.9116 (tt0) cc_final: 0.8820 (tm-30) REVERT: A 612 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8931 (mtpp) REVERT: B 160 GLN cc_start: 0.9124 (tt0) cc_final: 0.8822 (tm-30) REVERT: C 160 GLN cc_start: 0.9120 (tt0) cc_final: 0.8829 (tm-30) REVERT: D 58 LEU cc_start: 0.8692 (tt) cc_final: 0.8453 (tm) outliers start: 27 outliers final: 17 residues processed: 119 average time/residue: 1.1010 time to fit residues: 154.7659 Evaluate side-chains 109 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 5.9990 chunk 110 optimal weight: 50.0000 chunk 165 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 218 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22376 Z= 0.258 Angle : 0.483 7.782 30344 Z= 0.256 Chirality : 0.044 0.197 3568 Planarity : 0.003 0.029 3912 Dihedral : 3.774 16.586 3124 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.15 % Allowed : 12.95 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2884 helix: 2.23 (0.16), residues: 1116 sheet: 0.42 (0.22), residues: 512 loop : -1.01 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 278 HIS 0.002 0.001 HIS D 327 PHE 0.007 0.001 PHE B 43 TYR 0.009 0.001 TYR D 519 ARG 0.004 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLN cc_start: 0.9115 (tt0) cc_final: 0.8805 (tm-30) REVERT: A 612 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8927 (mtpp) REVERT: B 160 GLN cc_start: 0.9123 (tt0) cc_final: 0.8807 (tm-30) REVERT: B 278 TRP cc_start: 0.8766 (OUTLIER) cc_final: 0.8495 (t60) REVERT: C 160 GLN cc_start: 0.9118 (tt0) cc_final: 0.8808 (tm-30) REVERT: D 58 LEU cc_start: 0.8709 (tt) cc_final: 0.8454 (tm) outliers start: 27 outliers final: 18 residues processed: 114 average time/residue: 1.1274 time to fit residues: 151.3588 Evaluate side-chains 106 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 50.0000 chunk 265 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 233 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 22376 Z= 0.339 Angle : 0.518 8.479 30344 Z= 0.273 Chirality : 0.045 0.189 3568 Planarity : 0.003 0.029 3912 Dihedral : 3.928 16.947 3124 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.06 % Allowed : 13.12 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 2884 helix: 2.19 (0.16), residues: 1112 sheet: 0.40 (0.22), residues: 512 loop : -1.03 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 278 HIS 0.002 0.001 HIS D 327 PHE 0.007 0.001 PHE B 43 TYR 0.010 0.001 TYR A 519 ARG 0.004 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 2.508 Fit side-chains revert: symmetry clash REVERT: A 160 GLN cc_start: 0.9095 (tt0) cc_final: 0.8802 (tm-30) REVERT: A 300 GLU cc_start: 0.9153 (pt0) cc_final: 0.8724 (pp20) REVERT: A 612 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8934 (mtpp) REVERT: B 160 GLN cc_start: 0.9099 (tt0) cc_final: 0.8786 (tm-30) REVERT: B 612 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8948 (mtpp) REVERT: C 160 GLN cc_start: 0.9096 (tt0) cc_final: 0.8796 (tm-30) REVERT: C 300 GLU cc_start: 0.9188 (pt0) cc_final: 0.8690 (pp20) outliers start: 25 outliers final: 15 residues processed: 109 average time/residue: 1.2453 time to fit residues: 158.5912 Evaluate side-chains 104 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 30.0000 chunk 273 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 264 optimal weight: 0.2980 chunk 228 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS B 460 HIS C 460 HIS D 460 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22376 Z= 0.114 Angle : 0.447 7.600 30344 Z= 0.234 Chirality : 0.043 0.191 3568 Planarity : 0.003 0.028 3912 Dihedral : 3.576 15.610 3124 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.72 % Allowed : 13.63 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2884 helix: 2.30 (0.16), residues: 1116 sheet: 0.47 (0.22), residues: 508 loop : -0.92 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 278 HIS 0.002 0.000 HIS A 79 PHE 0.007 0.001 PHE B 43 TYR 0.017 0.001 TYR C 252 ARG 0.004 0.000 ARG D 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 2.817 Fit side-chains revert: symmetry clash REVERT: A 160 GLN cc_start: 0.9115 (tt0) cc_final: 0.8811 (tm-30) REVERT: A 300 GLU cc_start: 0.9132 (pt0) cc_final: 0.8618 (pp20) REVERT: B 160 GLN cc_start: 0.9127 (tt0) cc_final: 0.8803 (tm-30) REVERT: B 168 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 612 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8928 (mtpp) REVERT: C 160 GLN cc_start: 0.9117 (tt0) cc_final: 0.8807 (tm-30) REVERT: C 300 GLU cc_start: 0.9140 (pt0) cc_final: 0.8529 (pp20) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 1.1273 time to fit residues: 143.3896 Evaluate side-chains 106 residues out of total 2348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 50.0000 chunk 243 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 228 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069952 restraints weight = 43926.157| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.89 r_work: 0.2576 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 22376 Z= 0.408 Angle : 0.541 7.863 30344 Z= 0.284 Chirality : 0.046 0.172 3568 Planarity : 0.003 0.030 3912 Dihedral : 3.948 17.025 3124 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.89 % Allowed : 13.46 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.16), residues: 2884 helix: 2.26 (0.16), residues: 1104 sheet: 0.46 (0.22), residues: 512 loop : -0.94 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 278 HIS 0.003 0.001 HIS B 650 PHE 0.008 0.001 PHE B 43 TYR 0.017 0.001 TYR B 252 ARG 0.004 0.000 ARG D 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4690.85 seconds wall clock time: 85 minutes 12.73 seconds (5112.73 seconds total)