Starting phenix.real_space_refine (version: dev) on Sat Feb 25 09:21:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/02_2023/7mdo_23776_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/02_2023/7mdo_23776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/02_2023/7mdo_23776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/02_2023/7mdo_23776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/02_2023/7mdo_23776_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mdo_23776/02_2023/7mdo_23776_updated.pdb" } resolution = 4.12 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= 0.073 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 Process input model Symmetric amino acids flipped Residue "A ASP 205": "OD1" <-> "OD2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 671": "OD1" <-> "OD2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 751": "OD1" <-> "OD2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 534": "OE1" <-> "OE2" Residue "C ASP 671": "OD1" <-> "OD2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 751": "OD1" <-> "OD2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D ASP 393": "OD1" <-> "OD2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D ASP 671": "OD1" <-> "OD2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E ASP 393": "OD1" <-> "OD2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E ASP 671": "OD1" <-> "OD2" Residue "E PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 751": "OD1" <-> "OD2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F ASP 671": "OD1" <-> "OD2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 751": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 25098 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "B" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "C" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "D" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "E" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "F" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4156 Classifications: {'peptide': 531} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 502} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.73, per 1000 atoms: 0.55 Number of scatterers: 25098 At special positions: 0 Unit cell: (145.08, 141.96, 95.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 12 15.00 O 4788 8.00 N 4380 7.00 C 15786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.54 Conformation dependent library (CDL) restraints added in 3.6 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 18 sheets defined 45.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 5.353A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.611A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 322 through 333 removed outlier: 4.860A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.948A pdb=" N THR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 650 through 662 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 762 removed outlier: 3.909A pdb=" N ILE A 752 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG A 753 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET A 757 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 5.297A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.567A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 322 through 333 removed outlier: 4.829A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 650 through 662 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 684 through 702 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 749 through 762 removed outlier: 3.940A pdb=" N ILE B 752 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 753 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET B 757 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 5.407A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 229 through 232 No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.610A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 322 through 333 removed outlier: 4.884A pdb=" N GLN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 397 through 403 removed outlier: 3.543A pdb=" N THR C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 424 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 483 through 492 removed outlier: 3.552A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 527 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 650 through 662 Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 684 through 702 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 762 removed outlier: 3.990A pdb=" N ILE C 752 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG C 753 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET C 757 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 5.291A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 229 through 232 No H-bonds generated for 'chain 'D' and resid 229 through 232' Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.629A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 322 through 333 removed outlier: 4.850A pdb=" N GLN D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 385 removed outlier: 4.009A pdb=" N THR D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 408 through 424 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 483 through 492 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 599 through 607 Processing helix chain 'D' and resid 650 through 662 Processing helix chain 'D' and resid 672 through 676 Processing helix chain 'D' and resid 684 through 702 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 751 through 762 removed outlier: 4.146A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 5.377A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 229 through 232 No H-bonds generated for 'chain 'E' and resid 229 through 232' Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.586A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 322 through 325 No H-bonds generated for 'chain 'E' and resid 322 through 325' Processing helix chain 'E' and resid 328 through 333 removed outlier: 3.700A pdb=" N ASP E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 383 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 408 through 424 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 527 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 Processing helix chain 'E' and resid 579 through 581 No H-bonds generated for 'chain 'E' and resid 579 through 581' Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 650 through 662 Processing helix chain 'E' and resid 672 through 675 No H-bonds generated for 'chain 'E' and resid 672 through 675' Processing helix chain 'E' and resid 684 through 702 Processing helix chain 'E' and resid 732 through 740 Processing helix chain 'E' and resid 749 through 762 removed outlier: 4.027A pdb=" N ILE E 752 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG E 753 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET E 757 " --> pdb=" O LYS E 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 5.355A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 229 through 232 No H-bonds generated for 'chain 'F' and resid 229 through 232' Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.615A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 275 No H-bonds generated for 'chain 'F' and resid 273 through 275' Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 322 through 333 removed outlier: 4.854A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.956A pdb=" N THR F 385 " --> pdb=" O LEU F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 408 through 425 removed outlier: 3.571A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 527 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 579 through 581 No H-bonds generated for 'chain 'F' and resid 579 through 581' Processing helix chain 'F' and resid 599 through 607 Processing helix chain 'F' and resid 650 through 662 Processing helix chain 'F' and resid 672 through 676 Processing helix chain 'F' and resid 684 through 702 Processing helix chain 'F' and resid 733 through 740 Processing helix chain 'F' and resid 749 through 762 removed outlier: 3.911A pdb=" N ILE F 752 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG F 753 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET F 757 " --> pdb=" O LYS F 754 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 366 through 368 removed outlier: 5.740A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 515 through 517 removed outlier: 6.655A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 538 through 540 Processing sheet with id= D, first strand: chain 'B' and resid 366 through 368 removed outlier: 5.740A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 621 through 623 removed outlier: 3.708A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE B 643 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.511A pdb=" N ILE B 542 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 366 through 368 removed outlier: 5.644A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 621 through 623 Processing sheet with id= I, first strand: chain 'C' and resid 538 through 542 Processing sheet with id= J, first strand: chain 'D' and resid 366 through 368 removed outlier: 5.671A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 621 through 623 removed outlier: 3.699A pdb=" N GLY D 518 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 643 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 538 through 540 Processing sheet with id= M, first strand: chain 'E' and resid 366 through 368 removed outlier: 5.671A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 621 through 623 removed outlier: 3.765A pdb=" N GLY E 518 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 643 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 538 through 542 removed outlier: 3.529A pdb=" N ILE E 542 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 366 through 368 removed outlier: 5.633A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 621 through 623 removed outlier: 3.727A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE F 643 " --> pdb=" O TYR F 517 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 538 through 542 796 hydrogen bonds defined for protein. 2268 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: 8.10 Time building geometry restraints manager: 11.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8324 1.34 - 1.46: 3273 1.46 - 1.57: 13681 1.57 - 1.69: 18 1.69 - 1.81: 222 Bond restraints: 25518 Sorted by residual: bond pdb=" C TYR C 495 " pdb=" N PRO C 496 " ideal model delta sigma weight residual 1.336 1.357 -0.022 1.23e-02 6.61e+03 3.14e+00 bond pdb=" C TYR F 495 " pdb=" N PRO F 496 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 3.01e+00 bond pdb=" C TYR E 495 " pdb=" N PRO E 496 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.71e+00 bond pdb=" CA VAL B 343 " pdb=" CB VAL B 343 " ideal model delta sigma weight residual 1.533 1.552 -0.019 1.19e-02 7.06e+03 2.58e+00 bond pdb=" C TYR A 495 " pdb=" N PRO A 496 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.28e+00 ... (remaining 25513 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.78: 707 105.78 - 113.45: 13909 113.45 - 121.13: 13029 121.13 - 128.80: 6697 128.80 - 136.48: 140 Bond angle restraints: 34482 Sorted by residual: angle pdb=" N MET B 275 " pdb=" CA MET B 275 " pdb=" C MET B 275 " ideal model delta sigma weight residual 114.75 106.21 8.54 1.26e+00 6.30e-01 4.59e+01 angle pdb=" N MET E 275 " pdb=" CA MET E 275 " pdb=" C MET E 275 " ideal model delta sigma weight residual 114.75 106.24 8.51 1.26e+00 6.30e-01 4.56e+01 angle pdb=" N MET A 275 " pdb=" CA MET A 275 " pdb=" C MET A 275 " ideal model delta sigma weight residual 114.75 106.28 8.47 1.26e+00 6.30e-01 4.52e+01 angle pdb=" N MET C 275 " pdb=" CA MET C 275 " pdb=" C MET C 275 " ideal model delta sigma weight residual 114.75 106.56 8.19 1.26e+00 6.30e-01 4.22e+01 angle pdb=" N MET F 275 " pdb=" CA MET F 275 " pdb=" C MET F 275 " ideal model delta sigma weight residual 114.75 106.63 8.12 1.26e+00 6.30e-01 4.15e+01 ... (remaining 34477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 14728 25.08 - 50.17: 960 50.17 - 75.25: 103 75.25 - 100.33: 7 100.33 - 125.41: 6 Dihedral angle restraints: 15804 sinusoidal: 6612 harmonic: 9192 Sorted by residual: dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.41 -125.41 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1B ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PB ADP D 901 " pdb=" PA ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.16 -125.17 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.11 -125.12 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 15801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3339 0.083 - 0.166: 465 0.166 - 0.249: 62 0.249 - 0.332: 19 0.332 - 0.415: 9 Chirality restraints: 3894 Sorted by residual: chirality pdb=" CB ILE D 620 " pdb=" CA ILE D 620 " pdb=" CG1 ILE D 620 " pdb=" CG2 ILE D 620 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB ILE A 620 " pdb=" CA ILE A 620 " pdb=" CG1 ILE A 620 " pdb=" CG2 ILE A 620 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 3891 not shown) Planarity restraints: 4524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 327 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLN A 327 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN A 327 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU A 328 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 327 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C GLN E 327 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN E 327 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU E 328 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 327 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLN D 327 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN D 327 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU D 328 " 0.021 2.00e-02 2.50e+03 ... (remaining 4521 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6934 2.81 - 3.33: 24164 3.33 - 3.85: 43114 3.85 - 4.38: 49756 4.38 - 4.90: 79062 Nonbonded interactions: 203030 Sorted by model distance: nonbonded pdb=" O PRO F 246 " pdb=" OG1 THR F 249 " model vdw 2.283 2.440 nonbonded pdb=" O PRO C 246 " pdb=" OG1 THR C 249 " model vdw 2.286 2.440 nonbonded pdb=" O PRO B 246 " pdb=" OG1 THR B 249 " model vdw 2.291 2.440 nonbonded pdb=" O PRO E 246 " pdb=" OG1 THR E 249 " model vdw 2.293 2.440 nonbonded pdb=" O GLU F 546 " pdb=" OG1 THR F 549 " model vdw 2.303 2.440 ... (remaining 203025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 132 5.16 5 C 15786 2.51 5 N 4380 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.330 Check model and map are aligned: 0.360 Process input model: 62.350 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.005 0.045 25518 Z= 0.304 Angle : 1.058 12.067 34482 Z= 0.567 Chirality : 0.064 0.415 3894 Planarity : 0.008 0.084 4524 Dihedral : 15.751 125.415 9816 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.13), residues: 3150 helix: -2.46 (0.10), residues: 1590 sheet: -2.22 (0.27), residues: 336 loop : -0.88 (0.18), residues: 1224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 3.006 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 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: 0 outliers final: 0 residues processed: 954 average time/residue: 0.4599 time to fit residues: 647.6090 Evaluate side-chains 625 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 260 ASN B 285 ASN B 327 GLN B 421 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN C 421 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 337 GLN D 602 ASN E 285 ASN E 401 ASN E 533 ASN E 602 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS F 602 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 25518 Z= 0.312 Angle : 0.742 7.880 34482 Z= 0.385 Chirality : 0.045 0.177 3894 Planarity : 0.006 0.062 4524 Dihedral : 9.499 114.437 3480 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3150 helix: -0.92 (0.12), residues: 1566 sheet: -2.41 (0.26), residues: 342 loop : -0.40 (0.20), residues: 1242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 704 time to evaluate : 2.773 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 710 average time/residue: 0.4426 time to fit residues: 468.2000 Evaluate side-chains 538 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 535 time to evaluate : 2.840 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2344 time to fit residues: 5.1699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 240 optimal weight: 0.0770 chunk 196 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 312 optimal weight: 0.4980 chunk 257 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 232 optimal weight: 6.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 602 ASN B 602 ASN C 285 ASN C 499 HIS C 533 ASN C 602 ASN C 692 GLN D 533 ASN D 602 ASN E 215 GLN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 602 ASN F 285 ASN ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 25518 Z= 0.178 Angle : 0.671 10.424 34482 Z= 0.333 Chirality : 0.045 0.157 3894 Planarity : 0.006 0.116 4524 Dihedral : 9.101 115.650 3480 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3150 helix: -0.61 (0.13), residues: 1560 sheet: -2.18 (0.33), residues: 240 loop : -0.39 (0.19), residues: 1350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 708 time to evaluate : 3.002 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 711 average time/residue: 0.4552 time to fit residues: 488.6578 Evaluate side-chains 541 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 150 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 290 optimal weight: 8.9990 chunk 307 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 558 ASN B 602 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 558 ASN D 602 ASN E 285 ASN E 421 GLN E 602 ASN F 285 ASN F 602 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 25518 Z= 0.232 Angle : 0.678 7.355 34482 Z= 0.343 Chirality : 0.044 0.153 3894 Planarity : 0.005 0.104 4524 Dihedral : 8.906 112.865 3480 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 3150 helix: -0.41 (0.13), residues: 1560 sheet: -2.30 (0.27), residues: 306 loop : -0.08 (0.20), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 665 time to evaluate : 3.234 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 666 average time/residue: 0.4145 time to fit residues: 418.7040 Evaluate side-chains 520 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 519 time to evaluate : 3.147 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2102 time to fit residues: 4.3193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 262 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN D 602 ASN E 215 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 25518 Z= 0.229 Angle : 0.681 7.595 34482 Z= 0.342 Chirality : 0.045 0.199 3894 Planarity : 0.005 0.056 4524 Dihedral : 8.645 105.808 3480 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 3150 helix: -0.34 (0.13), residues: 1554 sheet: -2.27 (0.26), residues: 306 loop : -0.07 (0.20), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 653 time to evaluate : 2.951 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 revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.4092 time to fit residues: 404.5565 Evaluate side-chains 503 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 2.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 5.9990 chunk 276 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 142 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 558 ASN B 602 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 285 ASN D 602 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN E 602 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 25518 Z= 0.248 Angle : 0.695 8.230 34482 Z= 0.350 Chirality : 0.045 0.198 3894 Planarity : 0.005 0.044 4524 Dihedral : 8.535 104.481 3480 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 3150 helix: -0.35 (0.13), residues: 1536 sheet: -2.29 (0.26), residues: 312 loop : -0.02 (0.20), residues: 1302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 3.019 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 outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.4090 time to fit residues: 387.8775 Evaluate side-chains 484 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 3.062 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 175 optimal weight: 0.0970 chunk 224 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 306 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 760 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN D 602 ASN D 660 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN E 603 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 25518 Z= 0.256 Angle : 0.709 10.466 34482 Z= 0.355 Chirality : 0.045 0.177 3894 Planarity : 0.005 0.058 4524 Dihedral : 8.513 104.897 3480 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 3150 helix: -0.46 (0.13), residues: 1578 sheet: -2.23 (0.26), residues: 312 loop : 0.11 (0.21), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 3.038 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.4024 time to fit residues: 377.3913 Evaluate side-chains 475 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 151 optimal weight: 0.0570 chunk 28 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 602 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN D 533 ASN D 602 ASN E 327 GLN E 602 ASN F 340 HIS ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25518 Z= 0.185 Angle : 0.682 9.665 34482 Z= 0.337 Chirality : 0.045 0.172 3894 Planarity : 0.005 0.045 4524 Dihedral : 8.325 102.871 3480 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 3150 helix: -0.32 (0.13), residues: 1578 sheet: -2.15 (0.28), residues: 294 loop : 0.23 (0.20), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 635 time to evaluate : 3.063 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: 0 outliers final: 0 residues processed: 635 average time/residue: 0.4119 time to fit residues: 401.1980 Evaluate side-chains 478 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 3.027 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.5980 chunk 293 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 171 optimal weight: 0.0270 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 270 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN E 602 ASN F 285 ASN F 340 HIS F 494 GLN F 499 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25518 Z= 0.185 Angle : 0.697 9.546 34482 Z= 0.341 Chirality : 0.045 0.190 3894 Planarity : 0.005 0.045 4524 Dihedral : 8.230 102.537 3480 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 3150 helix: -0.31 (0.13), residues: 1578 sheet: -2.04 (0.28), residues: 294 loop : 0.28 (0.21), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 627 time to evaluate : 3.157 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: 1 outliers final: 0 residues processed: 627 average time/residue: 0.3960 time to fit residues: 383.5357 Evaluate side-chains 475 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 3.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 316 optimal weight: 0.8980 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 194 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN B 558 ASN B 602 ASN B 603 GLN C 340 HIS C 602 ASN C 660 ASN D 602 ASN E 602 ASN F 285 ASN F 340 HIS F 499 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 25518 Z= 0.233 Angle : 0.718 11.335 34482 Z= 0.358 Chirality : 0.046 0.162 3894 Planarity : 0.005 0.066 4524 Dihedral : 8.273 102.966 3480 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 3150 helix: -0.29 (0.13), residues: 1572 sheet: -2.02 (0.26), residues: 312 loop : 0.23 (0.21), residues: 1266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 609 time to evaluate : 2.789 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 outliers start: 0 outliers final: 0 residues processed: 609 average time/residue: 0.4105 time to fit residues: 383.9640 Evaluate side-chains 454 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 2.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 3.9990 chunk 268 optimal weight: 0.1980 chunk 77 optimal weight: 0.3980 chunk 232 optimal weight: 0.0470 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 252 optimal weight: 0.0060 chunk 105 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 0.0570 overall best weight: 0.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN B 602 ASN B 660 ASN C 602 ASN D 602 ASN E 602 ASN F 285 ASN F 327 GLN F 499 HIS ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.119198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098568 restraints weight = 77672.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101686 restraints weight = 45675.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.103768 restraints weight = 30890.645| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 25518 Z= 0.178 Angle : 0.708 9.238 34482 Z= 0.345 Chirality : 0.046 0.174 3894 Planarity : 0.005 0.045 4524 Dihedral : 8.057 100.154 3480 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 3150 helix: -0.10 (0.14), residues: 1542 sheet: -1.80 (0.28), residues: 300 loop : 0.08 (0.20), residues: 1308 =============================================================================== Job complete usr+sys time: 6813.81 seconds wall clock time: 124 minutes 18.69 seconds (7458.69 seconds total)