Starting phenix.real_space_refine on Wed Mar 4 17:13:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqr_23950/03_2026/7mqr_23950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqr_23950/03_2026/7mqr_23950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mqr_23950/03_2026/7mqr_23950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqr_23950/03_2026/7mqr_23950.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqr_23950/03_2026/7mqr_23950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqr_23950/03_2026/7mqr_23950.cif" } resolution = 4.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 9416 2.51 5 N 2518 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14878 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "E" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6664 Classifications: {'peptide': 823} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 778} Chain breaks: 5 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "G" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "H" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "I" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "J" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 6664 Classifications: {'peptide': 823} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 778} Chain breaks: 5 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 3.08, per 1000 atoms: 0.21 Number of scatterers: 14878 At special positions: 0 Unit cell: (94.185, 151.515, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2824 8.00 N 2518 7.00 C 9416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.04 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.02 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=1.96 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.04 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.10 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.04 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS H 7 " distance=2.09 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS H 19 " distance=2.10 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 11 " distance=2.04 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS J 7 " distance=1.97 Simple disulfide: pdb=" SG CYS I 20 " - pdb=" SG CYS J 19 " distance=1.97 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 860 " distance=2.03 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG E1001 " - " ASN E 255 " " NAG E1002 " - " ASN E 25 " " NAG E1003 " - " ASN E 215 " " NAG E1004 " - " ASN E 16 " " NAG E1005 " - " ASN E 606 " " NAG E1006 " - " ASN E 624 " " NAG E1007 " - " ASN E 397 " " NAG E1008 " - " ASN E 337 " " NAG E1009 " - " ASN E 418 " " NAG E1010 " - " ASN E 111 " " NAG F1001 " - " ASN F 255 " " NAG F1002 " - " ASN F 25 " " NAG F1003 " - " ASN F 215 " " NAG F1004 " - " ASN F 16 " " NAG F1005 " - " ASN F 606 " " NAG F1006 " - " ASN F 624 " " NAG F1007 " - " ASN F 397 " " NAG F1008 " - " ASN F 337 " " NAG F1009 " - " ASN F 418 " " NAG F1010 " - " ASN F 111 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 549.4 milliseconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 30 sheets defined 18.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'B' and resid 7 through 17 removed outlier: 4.034A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 23 removed outlier: 4.338A pdb=" N ARG E 19 " --> pdb=" O ASN E 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.583A pdb=" N PHE E 46 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 removed outlier: 4.121A pdb=" N ASP E 74 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.520A pdb=" N ASP E 142 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 143 " --> pdb=" O VAL E 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 139 through 143' Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 255 through 268 removed outlier: 3.790A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 350 through 358 Processing helix chain 'E' and resid 435 through 447 Processing helix chain 'E' and resid 496 through 500 Processing helix chain 'E' and resid 692 through 714 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'D' and resid 7 through 17 removed outlier: 4.033A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.838A pdb=" N GLU G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 18 Processing helix chain 'I' and resid 13 through 24 removed outlier: 3.838A pdb=" N GLU I 17 " --> pdb=" O LEU I 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 18 Processing helix chain 'F' and resid 16 through 23 removed outlier: 4.339A pdb=" N ARG F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS F 21 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU F 22 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.584A pdb=" N PHE F 46 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 4.121A pdb=" N ASP F 74 " --> pdb=" O SER F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 removed outlier: 3.520A pdb=" N ASP F 142 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN F 143 " --> pdb=" O VAL F 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 139 through 143' Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.790A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 350 through 358 Processing helix chain 'F' and resid 435 through 447 Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 692 through 714 Processing helix chain 'F' and resid 862 through 870 Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.592A pdb=" N LEU E 36 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 66 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL E 117 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL E 146 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 119 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.710A pdb=" N ILE E 57 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 82 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'E' and resid 212 through 216 removed outlier: 5.504A pdb=" N LEU E 213 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N CYS E 228 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN E 215 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'E' and resid 252 through 254 removed outlier: 6.960A pdb=" N HIS E 247 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 321 removed outlier: 6.577A pdb=" N VAL E 335 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 313 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN E 337 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU E 315 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER E 339 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY E 317 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 341 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS E 319 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LYS E 369 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 311 through 321 removed outlier: 6.577A pdb=" N VAL E 335 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 313 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN E 337 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU E 315 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER E 339 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY E 317 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE E 341 " --> pdb=" O GLY E 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS E 319 " --> pdb=" O ILE E 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'E' and resid 531 through 534 removed outlier: 3.773A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL E 588 " --> pdb=" O TYR E 562 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 602 through 604 removed outlier: 3.836A pdb=" N ILE E 602 " --> pdb=" O LYS E 614 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS E 614 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 604 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 633 " --> pdb=" O ARG E 780 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 788 " --> pdb=" O ARG E 794 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 633 " --> pdb=" O ARG E 780 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA E 803 " --> pdb=" O TYR E 779 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 818 through 822 Processing sheet with id=AB6, first strand: chain 'E' and resid 857 through 861 removed outlier: 4.002A pdb=" N PHE E 903 " --> pdb=" O TYR E 882 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 884 " --> pdb=" O THR E 901 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 901 " --> pdb=" O VAL E 884 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 12 through 14 removed outlier: 3.592A pdb=" N LEU F 36 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL F 117 " --> pdb=" O TYR F 144 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL F 146 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 119 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.708A pdb=" N ILE F 57 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 82 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 171 through 172 Processing sheet with id=AC1, first strand: chain 'F' and resid 212 through 216 removed outlier: 5.503A pdb=" N LEU F 213 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS F 228 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN F 215 " --> pdb=" O VAL F 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 231 through 233 Processing sheet with id=AC3, first strand: chain 'F' and resid 252 through 254 removed outlier: 6.961A pdb=" N HIS F 247 " --> pdb=" O CYS F 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 311 through 321 removed outlier: 6.576A pdb=" N VAL F 335 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N HIS F 313 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN F 337 " --> pdb=" O HIS F 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU F 315 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER F 339 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY F 317 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 341 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS F 319 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N LYS F 369 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU F 340 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ARG F 371 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE F 342 " --> pdb=" O ARG F 371 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 311 through 321 removed outlier: 6.576A pdb=" N VAL F 335 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N HIS F 313 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN F 337 " --> pdb=" O HIS F 313 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU F 315 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER F 339 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY F 317 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 341 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS F 319 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 485 through 487 Processing sheet with id=AC7, first strand: chain 'F' and resid 531 through 534 removed outlier: 3.773A pdb=" N GLY F 502 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE F 565 " --> pdb=" O PHE F 506 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL F 588 " --> pdb=" O TYR F 562 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 602 through 604 removed outlier: 3.836A pdb=" N ILE F 602 " --> pdb=" O LYS F 614 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS F 614 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 604 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL F 630 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 633 " --> pdb=" O ARG F 780 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN F 788 " --> pdb=" O ARG F 794 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.835A pdb=" N VAL F 630 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 633 " --> pdb=" O ARG F 780 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 803 " --> pdb=" O TYR F 779 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 818 through 822 Processing sheet with id=AD3, first strand: chain 'F' and resid 857 through 861 removed outlier: 4.002A pdb=" N PHE F 903 " --> pdb=" O TYR F 882 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL F 884 " --> pdb=" O THR F 901 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR F 901 " --> pdb=" O VAL F 884 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 954 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: 2.79 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4812 1.35 - 1.48: 3842 1.48 - 1.61: 6422 1.61 - 1.74: 0 1.74 - 1.87: 142 Bond restraints: 15218 Sorted by residual: bond pdb=" C1 NAG F1001 " pdb=" O5 NAG F1001 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1 NAG E1001 " pdb=" O5 NAG E1001 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C1 NAG E1002 " pdb=" O5 NAG E1002 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C1 NAG E1007 " pdb=" O5 NAG E1007 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.23e+01 ... (remaining 15213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.08: 20523 7.08 - 14.16: 97 14.16 - 21.25: 6 21.25 - 28.33: 2 28.33 - 35.41: 2 Bond angle restraints: 20630 Sorted by residual: angle pdb=" CG ARG F 774 " pdb=" CD ARG F 774 " pdb=" NE ARG F 774 " ideal model delta sigma weight residual 112.00 135.38 -23.38 2.20e+00 2.07e-01 1.13e+02 angle pdb=" CG ARG E 774 " pdb=" CD ARG E 774 " pdb=" NE ARG E 774 " ideal model delta sigma weight residual 112.00 135.33 -23.33 2.20e+00 2.07e-01 1.13e+02 angle pdb=" CA LEU J 15 " pdb=" CB LEU J 15 " pdb=" CG LEU J 15 " ideal model delta sigma weight residual 116.30 151.71 -35.41 3.50e+00 8.16e-02 1.02e+02 angle pdb=" CA LEU H 15 " pdb=" CB LEU H 15 " pdb=" CG LEU H 15 " ideal model delta sigma weight residual 116.30 151.66 -35.36 3.50e+00 8.16e-02 1.02e+02 angle pdb=" CA GLU C 17 " pdb=" CB GLU C 17 " pdb=" CG GLU C 17 " ideal model delta sigma weight residual 114.10 130.19 -16.09 2.00e+00 2.50e-01 6.48e+01 ... (remaining 20625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 8671 21.73 - 43.47: 708 43.47 - 65.20: 95 65.20 - 86.93: 28 86.93 - 108.67: 16 Dihedral angle restraints: 9518 sinusoidal: 4220 harmonic: 5298 Sorted by residual: dihedral pdb=" CB CYS G 20 " pdb=" SG CYS G 20 " pdb=" SG CYS H 19 " pdb=" CB CYS H 19 " ideal model delta sinusoidal sigma weight residual -86.00 -167.48 81.48 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CB CYS I 20 " pdb=" SG CYS I 20 " pdb=" SG CYS J 19 " pdb=" CB CYS J 19 " ideal model delta sinusoidal sigma weight residual -86.00 -165.10 79.10 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CA THR F 578 " pdb=" C THR F 578 " pdb=" N TYR F 579 " pdb=" CA TYR F 579 " ideal model delta harmonic sigma weight residual 180.00 136.61 43.39 0 5.00e+00 4.00e-02 7.53e+01 ... (remaining 9515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1994 0.099 - 0.198: 274 0.198 - 0.297: 42 0.297 - 0.396: 6 0.396 - 0.494: 4 Chirality restraints: 2320 Sorted by residual: chirality pdb=" CB ILE E 370 " pdb=" CA ILE E 370 " pdb=" CG1 ILE E 370 " pdb=" CG2 ILE E 370 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB VAL H 18 " pdb=" CA VAL H 18 " pdb=" CG1 VAL H 18 " pdb=" CG2 VAL H 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CB ILE F 370 " pdb=" CA ILE F 370 " pdb=" CG1 ILE F 370 " pdb=" CG2 ILE F 370 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.00e+00 ... (remaining 2317 not shown) Planarity restraints: 2652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 12 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C VAL H 12 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL H 12 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU H 13 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 12 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C VAL J 12 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL J 12 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU J 13 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 285 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO F 286 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 286 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 286 " -0.035 5.00e-02 4.00e+02 ... (remaining 2649 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5057 2.89 - 3.39: 12078 3.39 - 3.89: 25071 3.89 - 4.40: 26394 4.40 - 4.90: 44720 Nonbonded interactions: 113320 Sorted by model distance: nonbonded pdb=" O SER E 700 " pdb=" OG1 THR E 704 " model vdw 2.382 3.040 nonbonded pdb=" O SER F 700 " pdb=" OG1 THR F 704 " model vdw 2.382 3.040 nonbonded pdb=" O LYS E 310 " pdb=" OG1 THR E 334 " model vdw 2.394 3.040 nonbonded pdb=" O LYS F 310 " pdb=" OG1 THR F 334 " model vdw 2.394 3.040 nonbonded pdb=" OG1 THR E 889 " pdb=" OD1 ASN E 894 " model vdw 2.401 3.040 ... (remaining 113315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = (chain 'B' and resid 5 through 20) selection = (chain 'D' and resid 5 through 20) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.470 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 15286 Z= 0.363 Angle : 1.392 35.411 20786 Z= 0.678 Chirality : 0.072 0.494 2320 Planarity : 0.007 0.064 2632 Dihedral : 15.731 108.669 5950 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.72 % Favored : 89.94 % Rotamer: Outliers : 0.60 % Allowed : 0.85 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.17), residues: 1770 helix: -3.96 (0.17), residues: 256 sheet: -1.15 (0.28), residues: 328 loop : -2.34 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 774 TYR 0.023 0.002 TYR I 14 PHE 0.035 0.003 PHE E 497 TRP 0.011 0.001 TRP F 832 HIS 0.008 0.001 HIS F 775 Details of bonding type rmsd covalent geometry : bond 0.00741 (15218) covalent geometry : angle 1.32346 (20630) SS BOND : bond 0.02301 ( 48) SS BOND : angle 3.13735 ( 96) hydrogen bonds : bond 0.24854 ( 346) hydrogen bonds : angle 10.42967 ( 954) link_NAG-ASN : bond 0.01335 ( 20) link_NAG-ASN : angle 7.28848 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: E 442 MET cc_start: 0.8940 (ttp) cc_final: 0.8648 (tmm) REVERT: E 831 MET cc_start: 0.9581 (mmp) cc_final: 0.9364 (mmp) REVERT: C 17 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: H 15 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9049 (tp) REVERT: F 556 LEU cc_start: 0.8895 (mp) cc_final: 0.8672 (mp) outliers start: 10 outliers final: 3 residues processed: 104 average time/residue: 0.1006 time to fit residues: 16.8707 Evaluate side-chains 75 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 7.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 15 GLN E 108 ASN E 143 ASN E 295 ASN E 710 HIS C 5 GLN C 15 GLN F 143 ASN F 295 ASN F 710 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.090948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.060273 restraints weight = 66928.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.062224 restraints weight = 38205.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.063508 restraints weight = 27341.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.064282 restraints weight = 22380.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064703 restraints weight = 19909.659| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15286 Z= 0.136 Angle : 0.703 20.189 20786 Z= 0.344 Chirality : 0.046 0.206 2320 Planarity : 0.004 0.046 2632 Dihedral : 9.417 86.392 2396 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.50 % Favored : 93.28 % Rotamer: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.18), residues: 1770 helix: -2.36 (0.26), residues: 264 sheet: -0.72 (0.30), residues: 306 loop : -1.96 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 774 TYR 0.016 0.001 TYR E 91 PHE 0.016 0.001 PHE F 565 TRP 0.007 0.001 TRP E 414 HIS 0.010 0.001 HIS E 775 Details of bonding type rmsd covalent geometry : bond 0.00294 (15218) covalent geometry : angle 0.63714 (20630) SS BOND : bond 0.00435 ( 48) SS BOND : angle 1.12498 ( 96) hydrogen bonds : bond 0.04463 ( 346) hydrogen bonds : angle 6.88411 ( 954) link_NAG-ASN : bond 0.00864 ( 20) link_NAG-ASN : angle 5.42271 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 379 LEU cc_start: 0.9484 (mt) cc_final: 0.9279 (mt) REVERT: C 10 ILE cc_start: 0.8237 (mm) cc_final: 0.7686 (tp) REVERT: H 13 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7234 (tt0) REVERT: J 13 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7541 (tm-30) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.0914 time to fit residues: 14.7248 Evaluate side-chains 59 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 10 optimal weight: 0.0170 chunk 161 optimal weight: 9.9990 chunk 5 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN E 143 ASN E 264 HIS C 15 GLN F 108 ASN F 143 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.090840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.060008 restraints weight = 67152.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061926 restraints weight = 38309.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063202 restraints weight = 27514.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.063992 restraints weight = 22580.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.064414 restraints weight = 20089.118| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15286 Z= 0.118 Angle : 0.659 19.784 20786 Z= 0.318 Chirality : 0.045 0.192 2320 Planarity : 0.004 0.040 2632 Dihedral : 7.634 67.785 2396 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.89 % Favored : 92.88 % Rotamer: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.19), residues: 1770 helix: -1.40 (0.29), residues: 270 sheet: -0.37 (0.30), residues: 298 loop : -1.79 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 65 TYR 0.015 0.001 TYR F 91 PHE 0.015 0.001 PHE F 572 TRP 0.008 0.001 TRP E 414 HIS 0.003 0.001 HIS E 829 Details of bonding type rmsd covalent geometry : bond 0.00258 (15218) covalent geometry : angle 0.59511 (20630) SS BOND : bond 0.00341 ( 48) SS BOND : angle 0.90032 ( 96) hydrogen bonds : bond 0.03841 ( 346) hydrogen bonds : angle 6.16544 ( 954) link_NAG-ASN : bond 0.00835 ( 20) link_NAG-ASN : angle 5.23088 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: C 10 ILE cc_start: 0.8443 (mm) cc_final: 0.7890 (tp) REVERT: H 12 VAL cc_start: 0.9228 (p) cc_final: 0.8995 (p) REVERT: H 13 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7237 (tt0) REVERT: J 13 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7448 (tm-30) REVERT: F 11 MET cc_start: 0.8249 (pmm) cc_final: 0.7882 (pmm) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.0889 time to fit residues: 13.7419 Evaluate side-chains 57 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 147 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 156 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 HIS E 276 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** E 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 HIS F 264 HIS F 276 GLN ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN ** F 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.087143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057871 restraints weight = 67858.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057240 restraints weight = 42335.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057291 restraints weight = 35348.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057540 restraints weight = 33889.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057614 restraints weight = 31081.356| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15286 Z= 0.285 Angle : 0.789 10.381 20786 Z= 0.389 Chirality : 0.049 0.196 2320 Planarity : 0.005 0.051 2632 Dihedral : 7.595 68.871 2396 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.20), residues: 1770 helix: -0.78 (0.31), residues: 268 sheet: -0.64 (0.27), residues: 328 loop : -1.62 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 252 TYR 0.016 0.002 TYR F 91 PHE 0.028 0.002 PHE F 89 TRP 0.012 0.002 TRP E 529 HIS 0.009 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00616 (15218) covalent geometry : angle 0.76606 (20630) SS BOND : bond 0.00384 ( 48) SS BOND : angle 1.16161 ( 96) hydrogen bonds : bond 0.04348 ( 346) hydrogen bonds : angle 6.18454 ( 954) link_NAG-ASN : bond 0.00459 ( 20) link_NAG-ASN : angle 3.39755 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7214 (tt0) REVERT: J 13 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7477 (tm-30) REVERT: F 11 MET cc_start: 0.8435 (pmm) cc_final: 0.7864 (pmm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0929 time to fit residues: 11.7171 Evaluate side-chains 55 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN E 108 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN E 829 HIS C 15 GLN F 90 ASN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.089181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057581 restraints weight = 66734.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059420 restraints weight = 38257.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.060628 restraints weight = 27781.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061318 restraints weight = 23044.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.061776 restraints weight = 20691.532| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15286 Z= 0.111 Angle : 0.618 9.760 20786 Z= 0.307 Chirality : 0.046 0.198 2320 Planarity : 0.003 0.041 2632 Dihedral : 6.979 68.342 2396 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.61 % Favored : 93.16 % Rotamer: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.20), residues: 1770 helix: -0.11 (0.33), residues: 260 sheet: -0.57 (0.28), residues: 328 loop : -1.42 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 702 TYR 0.011 0.001 TYR F 849 PHE 0.012 0.001 PHE E 705 TRP 0.009 0.001 TRP E 559 HIS 0.003 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.00248 (15218) covalent geometry : angle 0.59176 (20630) SS BOND : bond 0.00271 ( 48) SS BOND : angle 0.94433 ( 96) hydrogen bonds : bond 0.03541 ( 346) hydrogen bonds : angle 5.80578 ( 954) link_NAG-ASN : bond 0.00503 ( 20) link_NAG-ASN : angle 3.26040 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7866 (mm-30) REVERT: H 13 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7201 (tt0) REVERT: J 13 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7385 (tm-30) REVERT: F 11 MET cc_start: 0.8415 (pmm) cc_final: 0.7907 (pmm) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.0862 time to fit residues: 12.5934 Evaluate side-chains 59 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 20 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN C 15 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.086970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057092 restraints weight = 67465.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057138 restraints weight = 41163.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056929 restraints weight = 34284.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057269 restraints weight = 33503.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057381 restraints weight = 29970.200| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15286 Z= 0.264 Angle : 0.751 8.967 20786 Z= 0.368 Chirality : 0.047 0.209 2320 Planarity : 0.004 0.063 2632 Dihedral : 7.326 70.123 2396 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.44 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.20), residues: 1770 helix: -0.27 (0.32), residues: 272 sheet: -0.64 (0.28), residues: 338 loop : -1.50 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 539 TYR 0.017 0.002 TYR F 91 PHE 0.018 0.002 PHE E 381 TRP 0.009 0.001 TRP E 414 HIS 0.014 0.001 HIS E 829 Details of bonding type rmsd covalent geometry : bond 0.00581 (15218) covalent geometry : angle 0.72824 (20630) SS BOND : bond 0.00299 ( 48) SS BOND : angle 1.10005 ( 96) hydrogen bonds : bond 0.03991 ( 346) hydrogen bonds : angle 6.08479 ( 954) link_NAG-ASN : bond 0.00522 ( 20) link_NAG-ASN : angle 3.30831 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8162 (mm-30) REVERT: H 13 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7356 (tt0) REVERT: J 13 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7478 (tm-30) REVERT: F 11 MET cc_start: 0.8379 (pmm) cc_final: 0.7803 (pmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0920 time to fit residues: 12.1130 Evaluate side-chains 55 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 2 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.088799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057858 restraints weight = 66564.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059623 restraints weight = 41429.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060098 restraints weight = 27292.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060408 restraints weight = 24862.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.060449 restraints weight = 23274.145| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15286 Z= 0.126 Angle : 0.636 9.338 20786 Z= 0.315 Chirality : 0.046 0.195 2320 Planarity : 0.003 0.042 2632 Dihedral : 6.966 69.426 2396 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.18 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.20), residues: 1770 helix: -0.10 (0.32), residues: 272 sheet: -0.61 (0.28), residues: 328 loop : -1.38 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 383 TYR 0.013 0.001 TYR C 14 PHE 0.011 0.001 PHE F 381 TRP 0.010 0.001 TRP E 559 HIS 0.009 0.001 HIS E 829 Details of bonding type rmsd covalent geometry : bond 0.00282 (15218) covalent geometry : angle 0.60413 (20630) SS BOND : bond 0.00256 ( 48) SS BOND : angle 1.02523 ( 96) hydrogen bonds : bond 0.03532 ( 346) hydrogen bonds : angle 5.76282 ( 954) link_NAG-ASN : bond 0.00433 ( 20) link_NAG-ASN : angle 3.58897 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.679 Fit side-chains REVERT: A 17 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8072 (mm-30) REVERT: H 13 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7265 (tt0) REVERT: J 13 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7505 (tm-30) REVERT: J 17 LEU cc_start: 0.6478 (mt) cc_final: 0.6206 (mt) REVERT: F 11 MET cc_start: 0.8354 (pmm) cc_final: 0.7816 (pmm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0898 time to fit residues: 12.3453 Evaluate side-chains 56 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 80 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 96 optimal weight: 0.0010 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.088497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.057443 restraints weight = 67163.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059247 restraints weight = 42062.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059591 restraints weight = 27608.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059947 restraints weight = 25485.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.059959 restraints weight = 23889.634| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15286 Z= 0.149 Angle : 0.663 10.525 20786 Z= 0.324 Chirality : 0.046 0.294 2320 Planarity : 0.003 0.042 2632 Dihedral : 7.005 69.018 2396 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.31 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1770 helix: -0.30 (0.32), residues: 284 sheet: -0.49 (0.28), residues: 314 loop : -1.38 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 65 TYR 0.011 0.001 TYR F 849 PHE 0.011 0.001 PHE E 565 TRP 0.010 0.001 TRP E 412 HIS 0.009 0.001 HIS E 829 Details of bonding type rmsd covalent geometry : bond 0.00331 (15218) covalent geometry : angle 0.62533 (20630) SS BOND : bond 0.00240 ( 48) SS BOND : angle 1.13140 ( 96) hydrogen bonds : bond 0.03508 ( 346) hydrogen bonds : angle 5.70283 ( 954) link_NAG-ASN : bond 0.00504 ( 20) link_NAG-ASN : angle 3.96857 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8146 (mm-30) REVERT: H 13 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7364 (tt0) REVERT: J 13 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7513 (tm-30) REVERT: J 17 LEU cc_start: 0.6407 (mt) cc_final: 0.6016 (mt) REVERT: F 11 MET cc_start: 0.8338 (pmm) cc_final: 0.7852 (pmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0880 time to fit residues: 12.0115 Evaluate side-chains 59 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 160 optimal weight: 0.5980 chunk 174 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS E 405 ASN C 15 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.089855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059182 restraints weight = 67243.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.061034 restraints weight = 42118.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.061322 restraints weight = 27820.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061633 restraints weight = 25796.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061814 restraints weight = 23142.978| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15286 Z= 0.098 Angle : 0.628 10.102 20786 Z= 0.308 Chirality : 0.047 0.357 2320 Planarity : 0.003 0.041 2632 Dihedral : 6.729 66.624 2396 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.29 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.20), residues: 1770 helix: -0.15 (0.31), residues: 284 sheet: -0.53 (0.28), residues: 328 loop : -1.32 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 65 TYR 0.014 0.001 TYR G 14 PHE 0.011 0.001 PHE E 427 TRP 0.010 0.001 TRP E 559 HIS 0.008 0.001 HIS E 829 Details of bonding type rmsd covalent geometry : bond 0.00218 (15218) covalent geometry : angle 0.59423 (20630) SS BOND : bond 0.00211 ( 48) SS BOND : angle 1.03287 ( 96) hydrogen bonds : bond 0.03258 ( 346) hydrogen bonds : angle 5.52996 ( 954) link_NAG-ASN : bond 0.00505 ( 20) link_NAG-ASN : angle 3.66015 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8031 (mm-30) REVERT: H 13 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7366 (tt0) REVERT: J 13 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7490 (tm-30) REVERT: F 11 MET cc_start: 0.8269 (pmm) cc_final: 0.7816 (pmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0870 time to fit residues: 12.8357 Evaluate side-chains 61 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 41 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 169 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.089795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059204 restraints weight = 67109.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060927 restraints weight = 42484.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061362 restraints weight = 28099.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061693 restraints weight = 25359.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.061711 restraints weight = 23789.795| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15286 Z= 0.111 Angle : 0.635 10.650 20786 Z= 0.309 Chirality : 0.048 0.495 2320 Planarity : 0.003 0.041 2632 Dihedral : 6.735 66.157 2396 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.74 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.20), residues: 1770 helix: -0.13 (0.31), residues: 286 sheet: -0.50 (0.28), residues: 328 loop : -1.29 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 804 TYR 0.040 0.001 TYR C 19 PHE 0.009 0.001 PHE E 565 TRP 0.012 0.001 TRP F 412 HIS 0.008 0.001 HIS E 829 Details of bonding type rmsd covalent geometry : bond 0.00249 (15218) covalent geometry : angle 0.60056 (20630) SS BOND : bond 0.00220 ( 48) SS BOND : angle 0.97614 ( 96) hydrogen bonds : bond 0.03258 ( 346) hydrogen bonds : angle 5.45836 ( 954) link_NAG-ASN : bond 0.00473 ( 20) link_NAG-ASN : angle 3.75838 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8045 (mm-30) REVERT: H 13 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7365 (tt0) REVERT: J 13 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7502 (tm-30) REVERT: J 17 LEU cc_start: 0.6530 (mt) cc_final: 0.6132 (mt) REVERT: F 11 MET cc_start: 0.8337 (pmm) cc_final: 0.7907 (pmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0881 time to fit residues: 11.9125 Evaluate side-chains 58 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 159 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 23 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN C 15 GLN F 328 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.088595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.056958 restraints weight = 66977.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058588 restraints weight = 41060.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059688 restraints weight = 30816.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.060335 restraints weight = 26060.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.060758 restraints weight = 23577.480| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15286 Z= 0.174 Angle : 0.665 10.847 20786 Z= 0.325 Chirality : 0.047 0.350 2320 Planarity : 0.003 0.042 2632 Dihedral : 6.858 66.942 2396 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.81 % Favored : 90.96 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.21), residues: 1770 helix: 0.23 (0.33), residues: 262 sheet: -0.49 (0.28), residues: 324 loop : -1.26 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 539 TYR 0.016 0.001 TYR C 19 PHE 0.016 0.001 PHE E 572 TRP 0.010 0.001 TRP E 414 HIS 0.010 0.001 HIS E 829 Details of bonding type rmsd covalent geometry : bond 0.00389 (15218) covalent geometry : angle 0.63527 (20630) SS BOND : bond 0.00293 ( 48) SS BOND : angle 1.02465 ( 96) hydrogen bonds : bond 0.03453 ( 346) hydrogen bonds : angle 5.54939 ( 954) link_NAG-ASN : bond 0.00474 ( 20) link_NAG-ASN : angle 3.56125 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.67 seconds wall clock time: 44 minutes 37.97 seconds (2677.97 seconds total)