Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 04:59:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ack_9594/07_2023/6ack_9594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ack_9594/07_2023/6ack_9594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ack_9594/07_2023/6ack_9594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ack_9594/07_2023/6ack_9594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ack_9594/07_2023/6ack_9594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ack_9594/07_2023/6ack_9594.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.908 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 164 5.16 5 C 18987 2.51 5 N 4918 2.21 5 O 5646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A ARG 1021": "NH1" <-> "NH2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1001": "NH1" <-> "NH2" Residue "B ARG 1021": "NH1" <-> "NH2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1021": "NH1" <-> "NH2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1073": "NH1" <-> "NH2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 29715 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8241 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1006} Chain breaks: 5 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 14.14, per 1000 atoms: 0.48 Number of scatterers: 29715 At special positions: 0 Unit cell: (145.2, 205.92, 196.68, 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 164 16.00 O 5646 8.00 N 4918 7.00 C 18987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.02 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.01 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.02 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.01 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.02 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.01 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.02 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.01 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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: 12.16 Conformation dependent library (CDL) restraints added in 4.2 seconds 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 45 sheets defined 28.0% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.319A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.539A pdb=" N THR A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 removed outlier: 4.370A pdb=" N ASN A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 901 through 922 removed outlier: 4.156A pdb=" N ALA A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 3.691A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.813A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1017 removed outlier: 4.211A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.693A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 373 through 377' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.623A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.761A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 765 Processing helix chain 'B' and resid 798 through 807 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 890 removed outlier: 3.694A pdb=" N PHE B 888 " --> pdb=" O MET B 884 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 890 " --> pdb=" O TYR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.579A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 900' Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.633A pdb=" N ALA B 912 " --> pdb=" O GLN B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 950 removed outlier: 4.213A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 965 removed outlier: 4.105A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1014 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.391A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 604 through 612 removed outlier: 3.903A pdb=" N THR C 608 " --> pdb=" O THR C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 808 Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 888 removed outlier: 3.637A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.766A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 900 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 895 through 901' Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.781A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 4.262A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 965 Processing helix chain 'C' and resid 968 through 1017 removed outlier: 3.561A pdb=" N GLU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.661A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 4.153A pdb=" N ASN D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.695A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.076A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.632A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.241A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 208 removed outlier: 3.638A pdb=" N ASP D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 207 " --> pdb=" O TRP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 252 removed outlier: 4.418A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.003A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 400 through 412 removed outlier: 4.065A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 4.217A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 466 removed outlier: 4.088A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.765A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 508' Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.057A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.665A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.074A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 4.034A pdb=" N SER D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.867A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.962A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.988A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 82 removed outlier: 4.137A pdb=" N SER A 111 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 130 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 222 removed outlier: 7.034A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 140 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA7, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 removed outlier: 7.007A pdb=" N GLY A 311 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASN A 528 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.612A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 629 removed outlier: 3.772A pdb=" N VAL A 628 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.705A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 659 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 650 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 700 through 701 Processing sheet with id=AB5, first strand: chain 'A' and resid 704 through 710 Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 710 removed outlier: 3.534A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB8, first strand: chain 'A' and resid 1063 through 1064 Processing sheet with id=AB9, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 34 removed outlier: 8.039A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 184 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 199 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 219 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 53 through 59 removed outlier: 4.192A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.861A pdb=" N ILE B 81 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 139 through 141 removed outlier: 6.594A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 298 through 304 removed outlier: 3.738A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 637 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 312 removed outlier: 6.516A pdb=" N GLY B 311 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN B 528 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.914A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 439 through 440 Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 652 removed outlier: 3.996A pdb=" N ILE B 650 " --> pdb=" O ALA B 658 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 700 through 701 removed outlier: 3.505A pdb=" N VAL B1050 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 705 through 709 Processing sheet with id=AD3, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD4, first strand: chain 'C' and resid 31 through 34 removed outlier: 7.916A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 34 removed outlier: 7.916A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 56 removed outlier: 4.118A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 5.544A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 298 through 306 removed outlier: 5.600A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER C 303 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 582 " --> pdb=" O LEU C 597 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AE1, first strand: chain 'C' and resid 341 through 345 removed outlier: 6.424A pdb=" N ASN C 424 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE C 361 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AE4, first strand: chain 'C' and resid 704 through 710 removed outlier: 3.691A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AE6, first strand: chain 'C' and resid 1078 through 1079 Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.976A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 1088 hydrogen bonds defined for protein. 3027 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: 11.22 Time building geometry restraints manager: 13.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 4899 1.26 - 1.40: 7920 1.40 - 1.55: 17381 1.55 - 1.70: 9 1.70 - 1.85: 231 Bond restraints: 30440 Sorted by residual: bond pdb=" C ALA C 676 " pdb=" O ALA C 676 " ideal model delta sigma weight residual 1.235 1.108 0.127 1.26e-02 6.30e+03 1.02e+02 bond pdb=" CA TYR C 677 " pdb=" C TYR C 677 " ideal model delta sigma weight residual 1.523 1.398 0.126 1.34e-02 5.57e+03 8.78e+01 bond pdb=" CA SER C 645 " pdb=" C SER C 645 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.74e+01 bond pdb=" CA TYR C 677 " pdb=" CB TYR C 677 " ideal model delta sigma weight residual 1.530 1.419 0.111 1.69e-02 3.50e+03 4.34e+01 bond pdb=" N SER C 645 " pdb=" CA SER C 645 " ideal model delta sigma weight residual 1.457 1.374 0.083 1.29e-02 6.01e+03 4.18e+01 ... (remaining 30435 not shown) Histogram of bond angle deviations from ideal: 94.55 - 102.62: 154 102.62 - 110.68: 9635 110.68 - 118.75: 14300 118.75 - 126.82: 16947 126.82 - 134.88: 380 Bond angle restraints: 41416 Sorted by residual: angle pdb=" N ILE A1112 " pdb=" CA ILE A1112 " pdb=" C ILE A1112 " ideal model delta sigma weight residual 113.20 102.43 10.77 9.60e-01 1.09e+00 1.26e+02 angle pdb=" C TYR C 646 " pdb=" N GLU C 647 " pdb=" CA GLU C 647 " ideal model delta sigma weight residual 122.79 109.06 13.73 1.63e+00 3.76e-01 7.10e+01 angle pdb=" O THR C 644 " pdb=" C THR C 644 " pdb=" N SER C 645 " ideal model delta sigma weight residual 122.91 132.25 -9.34 1.19e+00 7.06e-01 6.16e+01 angle pdb=" CA THR C 644 " pdb=" C THR C 644 " pdb=" N SER C 645 " ideal model delta sigma weight residual 114.98 104.49 10.49 1.34e+00 5.57e-01 6.13e+01 angle pdb=" N ILE A 891 " pdb=" CA ILE A 891 " pdb=" C ILE A 891 " ideal model delta sigma weight residual 112.90 106.04 6.86 9.60e-01 1.09e+00 5.11e+01 ... (remaining 41411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 16900 17.50 - 34.99: 987 34.99 - 52.49: 151 52.49 - 69.99: 28 69.99 - 87.48: 12 Dihedral angle restraints: 18078 sinusoidal: 7038 harmonic: 11040 Sorted by residual: dihedral pdb=" CA GLU B1074 " pdb=" C GLU B1074 " pdb=" N GLY B1075 " pdb=" CA GLY B1075 " ideal model delta harmonic sigma weight residual 180.00 -117.27 -62.73 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -117.49 -62.51 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA GLY B 726 " pdb=" C GLY B 726 " pdb=" N ASP B 727 " pdb=" CA ASP B 727 " ideal model delta harmonic sigma weight residual 180.00 125.46 54.54 0 5.00e+00 4.00e-02 1.19e+02 ... (remaining 18075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 4383 0.135 - 0.269: 238 0.269 - 0.404: 5 0.404 - 0.538: 0 0.538 - 0.673: 2 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CA TYR C 646 " pdb=" N TYR C 646 " pdb=" C TYR C 646 " pdb=" CB TYR C 646 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA TYR C 677 " pdb=" N TYR C 677 " pdb=" C TYR C 677 " pdb=" CB TYR C 677 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" CG LEU C 846 " pdb=" CB LEU C 846 " pdb=" CD1 LEU C 846 " pdb=" CD2 LEU C 846 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 4625 not shown) Planarity restraints: 5366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 677 " -0.018 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR C 677 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR C 677 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 677 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 677 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 677 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR C 677 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR C 677 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 644 " -0.018 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C THR C 644 " 0.070 2.00e-02 2.50e+03 pdb=" O THR C 644 " -0.029 2.00e-02 2.50e+03 pdb=" N SER C 645 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 585 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO B 586 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 586 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 586 " -0.047 5.00e-02 4.00e+02 ... (remaining 5363 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 13 2.21 - 2.88: 11783 2.88 - 3.55: 43295 3.55 - 4.23: 74277 4.23 - 4.90: 119315 Nonbonded interactions: 248683 Sorted by model distance: nonbonded pdb=" O SER C 659 " pdb=" CG2 ILE C 674 " model vdw 1.533 3.460 nonbonded pdb=" O TYR C 646 " pdb=" OG SER C 680 " model vdw 1.617 2.440 nonbonded pdb=" CB TYR C 646 " pdb=" CE2 TYR C 677 " model vdw 2.022 3.740 nonbonded pdb=" O GLY C 655 " pdb=" O THR C 678 " model vdw 2.083 3.040 nonbonded pdb=" O THR C 644 " pdb=" O SER C 645 " model vdw 2.115 3.040 ... (remaining 248678 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 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = (chain 'B' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 8.100 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 73.700 Find NCS groups from input model: 1.780 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.010 0.147 30440 Z= 0.677 Angle : 1.348 13.734 41416 Z= 0.764 Chirality : 0.068 0.673 4628 Planarity : 0.009 0.087 5366 Dihedral : 11.386 80.555 10850 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 16.09 % Favored : 83.46 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 2.23 % Twisted General : 1.14 % 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: -4.81 (0.11), residues: 3754 helix: -2.49 (0.12), residues: 978 sheet: -2.40 (0.21), residues: 498 loop : -3.93 (0.10), residues: 2278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 488 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 513 average time/residue: 0.4447 time to fit residues: 354.8617 Evaluate side-chains 276 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 266 time to evaluate : 3.529 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2635 time to fit residues: 9.9665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 341 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 155 ASN A 181 HIS A 230 ASN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 505 ASN A 627 ASN A 691 ASN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN A1040 HIS B 70 HIS B 155 ASN B 214 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS B 479 ASN ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN B 733 ASN B 737 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B 877 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN C 445 HIS C 473 ASN C 479 ASN C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN C 877 GLN C 935 ASN ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN C1005 ASN C1088 GLN ** C1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 250 ASN D 417 HIS D 522 GLN D 526 GLN D 572 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 30440 Z= 0.281 Angle : 0.784 10.806 41416 Z= 0.418 Chirality : 0.048 0.261 4628 Planarity : 0.006 0.060 5366 Dihedral : 8.047 60.470 4064 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.97 % Favored : 86.71 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.07 (0.12), residues: 3754 helix: -1.47 (0.14), residues: 999 sheet: -2.17 (0.22), residues: 479 loop : -3.62 (0.11), residues: 2276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 379 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 386 average time/residue: 0.4037 time to fit residues: 254.6292 Evaluate side-chains 257 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 3.610 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4381 time to fit residues: 8.3450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 342 optimal weight: 30.0000 chunk 369 optimal weight: 20.0000 chunk 304 optimal weight: 0.8980 chunk 339 optimal weight: 50.0000 chunk 116 optimal weight: 0.0670 chunk 274 optimal weight: 0.9980 overall best weight: 1.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN A 756 GLN A 759 ASN A 806 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 147 GLN B 214 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 699 ASN C 744 GLN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN D 117 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 30440 Z= 0.216 Angle : 0.709 9.041 41416 Z= 0.376 Chirality : 0.047 0.196 4628 Planarity : 0.005 0.062 5366 Dihedral : 7.232 61.300 4064 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.81 % Favored : 86.89 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.62 (0.12), residues: 3754 helix: -0.87 (0.15), residues: 996 sheet: -1.96 (0.22), residues: 481 loop : -3.43 (0.11), residues: 2277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 366 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 369 average time/residue: 0.4155 time to fit residues: 250.5051 Evaluate side-chains 249 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 246 time to evaluate : 3.524 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2843 time to fit residues: 6.3272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 50.0000 chunk 257 optimal weight: 40.0000 chunk 177 optimal weight: 3.9990 chunk 37 optimal weight: 0.0060 chunk 163 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 343 optimal weight: 0.0040 chunk 363 optimal weight: 4.9990 chunk 179 optimal weight: 0.3980 chunk 325 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 ASN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN A 942 ASN A1095 GLN B 70 HIS B 304 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 GLN B1040 HIS ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 HIS C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 30440 Z= 0.170 Angle : 0.661 9.966 41416 Z= 0.348 Chirality : 0.046 0.192 4628 Planarity : 0.005 0.064 5366 Dihedral : 6.585 58.637 4064 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.35 % Favored : 88.44 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.18 (0.13), residues: 3754 helix: -0.35 (0.16), residues: 998 sheet: -1.87 (0.21), residues: 556 loop : -3.21 (0.12), residues: 2200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 400 average time/residue: 0.3932 time to fit residues: 257.1073 Evaluate side-chains 261 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 259 time to evaluate : 3.444 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3126 time to fit residues: 5.9918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 270 optimal weight: 9.9990 chunk 149 optimal weight: 0.0070 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 185 optimal weight: 0.5980 chunk 326 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 3.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN B 147 GLN B 214 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 GLN B1088 GLN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN D 330 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 30440 Z= 0.291 Angle : 0.734 11.739 41416 Z= 0.386 Chirality : 0.047 0.279 4628 Planarity : 0.005 0.058 5366 Dihedral : 6.654 56.084 4064 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.67 % Favored : 86.07 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.28 (0.13), residues: 3754 helix: -0.50 (0.16), residues: 996 sheet: -1.95 (0.22), residues: 522 loop : -3.23 (0.12), residues: 2236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 319 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 320 average time/residue: 0.4135 time to fit residues: 220.2520 Evaluate side-chains 224 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 4.006 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3452 time to fit residues: 7.4159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 9.9990 chunk 327 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 190 optimal weight: 0.0670 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 ASN B 759 ASN B1088 GLN B1090 ASN ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 30440 Z= 0.203 Angle : 0.671 10.379 41416 Z= 0.352 Chirality : 0.046 0.308 4628 Planarity : 0.005 0.061 5366 Dihedral : 6.439 56.651 4064 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.44 % Favored : 87.32 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.08 (0.13), residues: 3754 helix: -0.27 (0.16), residues: 995 sheet: -1.70 (0.23), residues: 486 loop : -3.14 (0.12), residues: 2273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 334 time to evaluate : 3.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 335 average time/residue: 0.4093 time to fit residues: 227.3674 Evaluate side-chains 236 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 3.446 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3321 time to fit residues: 5.1516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 0.4980 chunk 265 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 362 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A 993 GLN ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 304 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 30440 Z= 0.294 Angle : 0.735 11.919 41416 Z= 0.387 Chirality : 0.047 0.226 4628 Planarity : 0.005 0.058 5366 Dihedral : 6.576 55.630 4064 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.36 % Favored : 85.35 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.15 (0.13), residues: 3754 helix: -0.41 (0.16), residues: 985 sheet: -1.77 (0.23), residues: 496 loop : -3.14 (0.12), residues: 2273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 307 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 0.4226 time to fit residues: 221.8363 Evaluate side-chains 221 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 3.572 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3185 time to fit residues: 5.4928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 20.0000 chunk 144 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 109 optimal weight: 0.0470 chunk 71 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 246 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 284 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN B1090 ASN ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN D 103 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 30440 Z= 0.179 Angle : 0.668 11.761 41416 Z= 0.350 Chirality : 0.046 0.232 4628 Planarity : 0.005 0.062 5366 Dihedral : 6.224 55.706 4064 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.80 % Favored : 87.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.90 (0.13), residues: 3754 helix: 0.02 (0.16), residues: 977 sheet: -1.65 (0.23), residues: 528 loop : -3.08 (0.12), residues: 2249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.4240 time to fit residues: 236.4364 Evaluate side-chains 231 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.698 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 8.9990 chunk 347 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 337 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 103 optimal weight: 0.0980 chunk 305 optimal weight: 0.8980 chunk 319 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 401 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN B1088 GLN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 ASN ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 30440 Z= 0.233 Angle : 0.697 12.639 41416 Z= 0.364 Chirality : 0.046 0.194 4628 Planarity : 0.005 0.061 5366 Dihedral : 6.205 54.923 4064 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.16 % Favored : 86.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.83 (0.13), residues: 3754 helix: 0.05 (0.16), residues: 965 sheet: -1.57 (0.24), residues: 502 loop : -3.01 (0.12), residues: 2287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.4165 time to fit residues: 207.0517 Evaluate side-chains 213 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.701 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 20.0000 chunk 357 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 374 optimal weight: 30.0000 chunk 344 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 230 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN D 103 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 30440 Z= 0.349 Angle : 0.814 15.330 41416 Z= 0.427 Chirality : 0.049 0.250 4628 Planarity : 0.006 0.059 5366 Dihedral : 6.752 53.406 4064 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 15.29 % Favored : 84.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.19 (0.13), residues: 3754 helix: -0.52 (0.16), residues: 998 sheet: -1.79 (0.23), residues: 491 loop : -3.13 (0.12), residues: 2265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.4132 time to fit residues: 194.9427 Evaluate side-chains 207 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.756 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 306 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 55 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN A 759 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.091699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.068664 restraints weight = 182534.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.067671 restraints weight = 131712.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.068483 restraints weight = 111798.577| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 30440 Z= 0.250 Angle : 0.728 15.029 41416 Z= 0.380 Chirality : 0.047 0.239 4628 Planarity : 0.005 0.059 5366 Dihedral : 6.493 53.920 4064 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.48 % Favored : 86.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.13), residues: 3754 helix: -0.19 (0.16), residues: 978 sheet: -1.74 (0.23), residues: 510 loop : -3.07 (0.12), residues: 2266 =============================================================================== Job complete usr+sys time: 5577.53 seconds wall clock time: 103 minutes 39.20 seconds (6219.20 seconds total)