Starting phenix.real_space_refine on Fri Jul 3 16:39:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqr_23950/07_2026/7mqr_23950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqr_23950/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mqr_23950/07_2026/7mqr_23950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqr_23950/07_2026/7mqr_23950.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mqr_23950/07_2026/7mqr_23950.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqr_23950/07_2026/7mqr_23950.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqr_23950/07_2026/7mqr_23950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqr_23950/07_2026/7mqr_23950.map" } 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-6108/lib/python3.11/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 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 chiralities: 10 Time building chain proxies: 3.43, per 1000 atoms: 0.23 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: 0.71 Conformation dependent library (CDL) restraints added in 476.0 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: 0.58 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: 2.47 Time building geometry restraints manager: 1.05 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 - 17.30: 8034 17.30 - 34.60: 851 34.60 - 51.90: 155 51.90 - 69.20: 40 69.20 - 86.50: 18 Dihedral angle restraints: 9098 sinusoidal: 3800 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 9095 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 14.721 86.496 5530 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/Z covalent geometry : bond 0.00741 / 0.36 (15218) covalent geometry : angle 1.32346 / 0.66 (20630) SS BOND : bond 0.02301 / 1.45 ( 48) SS BOND : angle 3.13735 / 1.99 ( 96) hydrogen bonds : bond 0.24854 / 16.39 ( 346) hydrogen bonds : angle 10.42967 / 7.16 ( 954) link_NAG-ASN : bond 0.01335 / 0.69 ( 20) link_NAG-ASN : angle 7.28848 / 5.05 ( 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 : 0.593 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: 0.0926 time to fit residues: 15.5657 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 : 0.425 ------------------------------------------------------------------------------- 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... 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 108 ASN F 143 ASN F 295 ASN F 710 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.090980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.060262 restraints weight = 67155.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062207 restraints weight = 38449.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.063486 restraints weight = 27557.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.064251 restraints weight = 22596.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.064670 restraints weight = 20102.234| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1363 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= 0.139 Angle : 0.701 20.239 20786 Z= 0.347 Chirality : 0.046 0.208 2320 Planarity : 0.005 0.069 2632 Dihedral : 5.707 27.471 1976 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.55 % Favored : 93.22 % Rotamer: Outliers : 0.12 % Allowed : 3.20 % 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: -2.64 (0.18), residues: 1770 helix: -2.44 (0.26), residues: 264 sheet: -0.68 (0.29), residues: 326 loop : -2.01 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 774 TYR 0.016 0.001 TYR E 91 PHE 0.015 0.001 PHE F 565 TRP 0.006 0.001 TRP E 414 HIS 0.009 0.001 HIS E 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (15218) covalent geometry : angle 0.63599 / 0.33 (20630) SS BOND : bond 0.00357 / 0.23 ( 48) SS BOND : angle 1.08341 / 0.76 ( 96) hydrogen bonds : bond 0.04688 / 2.92 ( 346) hydrogen bonds : angle 6.93032 / 4.74 ( 954) link_NAG-ASN : bond 0.00873 / 0.46 ( 20) link_NAG-ASN : angle 5.41267 / 3.75 ( 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: 2 poor density : 91 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 379 LEU cc_start: 0.9476 (mt) cc_final: 0.9267 (mt) REVERT: C 10 ILE cc_start: 0.8231 (mm) cc_final: 0.7680 (tp) REVERT: H 13 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7229 (tt0) REVERT: J 13 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7540 (tm-30) outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.0775 time to fit residues: 12.4587 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 : 0.581 ------------------------------------------------------------------------------- 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: 8.9990 chunk 5 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN E 143 ASN C 15 GLN F 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.091540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061313 restraints weight = 67604.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.063534 restraints weight = 41232.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.064978 restraints weight = 26308.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064866 restraints weight = 22848.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065025 restraints weight = 21912.166| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1755 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= 0.103 Angle : 0.636 19.595 20786 Z= 0.311 Chirality : 0.045 0.186 2320 Planarity : 0.003 0.041 2632 Dihedral : 5.148 28.576 1976 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.72 % Favored : 93.05 % Rotamer: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % 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: -2.18 (0.19), residues: 1770 helix: -1.51 (0.29), residues: 266 sheet: -0.51 (0.30), residues: 308 loop : -1.78 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 774 TYR 0.013 0.001 TYR F 91 PHE 0.015 0.001 PHE E 572 TRP 0.007 0.001 TRP E 414 HIS 0.003 0.001 HIS E 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (15218) covalent geometry : angle 0.57564 / 0.30 (20630) SS BOND : bond 0.00276 / 0.17 ( 48) SS BOND : angle 0.93000 / 0.64 ( 96) hydrogen bonds : bond 0.03768 / 2.35 ( 346) hydrogen bonds : angle 6.20230 / 4.28 ( 954) link_NAG-ASN : bond 0.00836 / 0.42 ( 20) link_NAG-ASN : angle 5.00181 / 3.48 ( 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 : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 ILE cc_start: 0.8331 (mm) cc_final: 0.7797 (tp) REVERT: H 13 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7240 (tt0) REVERT: J 13 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7530 (tm-30) REVERT: J 15 LEU cc_start: 0.9539 (tp) cc_final: 0.9290 (pp) REVERT: F 11 MET cc_start: 0.8209 (pmm) cc_final: 0.7879 (pmm) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.0881 time to fit residues: 13.6251 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 : 0.531 ------------------------------------------------------------------------------- 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: 10.0000 chunk 141 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN E 185 HIS ** E 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 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 108 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.086134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055417 restraints weight = 68009.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.055686 restraints weight = 45850.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055976 restraints weight = 34050.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056323 restraints weight = 32143.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056371 restraints weight = 28871.310| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 15286 Z= 0.350 Angle : 0.885 10.835 20786 Z= 0.434 Chirality : 0.050 0.269 2320 Planarity : 0.005 0.054 2632 Dihedral : 5.802 23.885 1976 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.60 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -2.00 (0.20), residues: 1770 helix: -0.97 (0.30), residues: 270 sheet: -0.71 (0.27), residues: 338 loop : -1.68 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 702 TYR 0.023 0.002 TYR F 67 PHE 0.034 0.003 PHE E 89 TRP 0.015 0.002 TRP E 529 HIS 0.010 0.002 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.35 (15218) covalent geometry : angle 0.86352 / 0.43 (20630) SS BOND : bond 0.00498 / 0.34 ( 48) SS BOND : angle 1.26122 / 0.88 ( 96) hydrogen bonds : bond 0.04780 / 3.04 ( 346) hydrogen bonds : angle 6.37644 / 4.33 ( 954) link_NAG-ASN : bond 0.00856 / 0.41 ( 20) link_NAG-ASN : angle 3.54821 / 2.44 ( 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 69 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7215 (tt0) REVERT: H 15 LEU cc_start: 0.9419 (pp) cc_final: 0.9199 (tp) REVERT: J 13 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7490 (tm-30) REVERT: F 11 MET cc_start: 0.8440 (pmm) cc_final: 0.7840 (pmm) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0929 time to fit residues: 11.1411 Evaluate side-chains 52 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN E 108 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN E 328 GLN C 15 GLN F 90 ASN F 108 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.088871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.057943 restraints weight = 66717.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059625 restraints weight = 43031.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.060119 restraints weight = 27900.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060492 restraints weight = 25450.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060410 restraints weight = 23606.564| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2831 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= 0.112 Angle : 0.611 8.417 20786 Z= 0.309 Chirality : 0.045 0.187 2320 Planarity : 0.003 0.042 2632 Dihedral : 5.136 27.514 1976 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.95 % Favored : 92.82 % Rotamer: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.40 % 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: -1.52 (0.20), residues: 1770 helix: -0.06 (0.33), residues: 256 sheet: -0.58 (0.29), residues: 318 loop : -1.41 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 804 TYR 0.011 0.001 TYR F 849 PHE 0.012 0.001 PHE E 572 TRP 0.011 0.001 TRP E 559 HIS 0.005 0.001 HIS E 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15218) covalent geometry : angle 0.59250 / 0.30 (20630) SS BOND : bond 0.00271 / 0.17 ( 48) SS BOND : angle 0.89218 / 0.64 ( 96) hydrogen bonds : bond 0.03599 / 2.26 ( 346) hydrogen bonds : angle 5.86866 / 3.99 ( 954) link_NAG-ASN : bond 0.00435 / 0.28 ( 20) link_NAG-ASN : angle 2.74408 / 1.96 ( 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 82 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7918 (mm-30) REVERT: H 13 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7233 (tt0) REVERT: J 13 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7419 (tm-30) REVERT: F 11 MET cc_start: 0.8383 (pmm) cc_final: 0.7838 (pmm) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.0899 time to fit residues: 12.6832 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 : 0.667 ------------------------------------------------------------------------------- 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: 9.9990 chunk 119 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN C 15 GLN ** 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 = 0.3878 r_free = 0.3878 target = 0.086965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056470 restraints weight = 67304.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056806 restraints weight = 45014.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057239 restraints weight = 32207.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057549 restraints weight = 30938.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057671 restraints weight = 28233.289| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15286 Z= 0.248 Angle : 0.743 8.940 20786 Z= 0.363 Chirality : 0.047 0.202 2320 Planarity : 0.004 0.055 2632 Dihedral : 5.360 28.007 1976 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.83 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -1.63 (0.20), residues: 1770 helix: -0.19 (0.32), residues: 272 sheet: -0.66 (0.28), residues: 328 loop : -1.50 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 83 TYR 0.018 0.002 TYR F 91 PHE 0.018 0.002 PHE F 381 TRP 0.009 0.001 TRP E 414 HIS 0.006 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (15218) covalent geometry : angle 0.71187 / 0.36 (20630) SS BOND : bond 0.00377 / 0.20 ( 48) SS BOND : angle 1.08281 / 0.77 ( 96) hydrogen bonds : bond 0.03965 / 2.50 ( 346) hydrogen bonds : angle 6.06755 / 4.11 ( 954) link_NAG-ASN : bond 0.00561 / 0.31 ( 20) link_NAG-ASN : angle 3.87317 / 2.66 ( 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 : 0.622 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8156 (mm-30) REVERT: E 80 THR cc_start: 0.8371 (p) cc_final: 0.8167 (p) REVERT: H 13 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7332 (tt0) REVERT: J 13 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7520 (tm-30) REVERT: J 17 LEU cc_start: 0.6320 (mt) cc_final: 0.6025 (mt) REVERT: F 11 MET cc_start: 0.8353 (pmm) cc_final: 0.7771 (pmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0873 time to fit residues: 11.5476 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 : 0.443 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3896 r_free = 0.3896 target = 0.087912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057902 restraints weight = 66697.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058256 restraints weight = 40028.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058504 restraints weight = 31675.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058817 restraints weight = 30096.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058870 restraints weight = 27048.976| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15286 Z= 0.186 Angle : 0.660 8.997 20786 Z= 0.331 Chirality : 0.046 0.192 2320 Planarity : 0.004 0.043 2632 Dihedral : 5.212 30.466 1976 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.81 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: -1.48 (0.20), residues: 1770 helix: -0.02 (0.33), residues: 268 sheet: -0.56 (0.29), residues: 304 loop : -1.39 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 383 TYR 0.014 0.001 TYR G 14 PHE 0.015 0.001 PHE F 381 TRP 0.010 0.001 TRP F 412 HIS 0.006 0.001 HIS F 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (15218) covalent geometry : angle 0.63621 / 0.33 (20630) SS BOND : bond 0.00297 / 0.19 ( 48) SS BOND : angle 1.16473 / 0.82 ( 96) hydrogen bonds : bond 0.03713 / 2.34 ( 346) hydrogen bonds : angle 5.84794 / 3.95 ( 954) link_NAG-ASN : bond 0.00455 / 0.27 ( 20) link_NAG-ASN : angle 3.07606 / 2.16 ( 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 81 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8198 (mm-30) REVERT: H 13 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7427 (tt0) REVERT: J 13 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7501 (tm-30) REVERT: J 17 LEU cc_start: 0.6450 (mt) cc_final: 0.6158 (mt) REVERT: F 11 MET cc_start: 0.8378 (pmm) cc_final: 0.7820 (pmm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0896 time to fit residues: 12.5189 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 : 0.498 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** E 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.087403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055254 restraints weight = 67228.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056934 restraints weight = 40304.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058012 restraints weight = 29931.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058734 restraints weight = 25176.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059074 restraints weight = 22649.446| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15286 Z= 0.214 Angle : 0.697 9.991 20786 Z= 0.346 Chirality : 0.046 0.206 2320 Planarity : 0.004 0.044 2632 Dihedral : 5.308 32.662 1976 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.23 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -1.56 (0.20), residues: 1770 helix: -0.19 (0.32), residues: 272 sheet: -0.69 (0.27), residues: 330 loop : -1.40 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 114 TYR 0.014 0.001 TYR F 91 PHE 0.017 0.002 PHE E 382 TRP 0.011 0.001 TRP E 529 HIS 0.005 0.001 HIS E 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (15218) covalent geometry : angle 0.67569 / 0.34 (20630) SS BOND : bond 0.00281 / 0.17 ( 48) SS BOND : angle 1.35059 / 0.90 ( 96) hydrogen bonds : bond 0.03846 / 2.41 ( 346) hydrogen bonds : angle 5.94585 / 4.01 ( 954) link_NAG-ASN : bond 0.00433 / 0.26 ( 20) link_NAG-ASN : angle 2.87723 / 2.03 ( 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 73 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.618 Fit side-chains REVERT: A 17 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8264 (mm-30) REVERT: E 80 THR cc_start: 0.8344 (p) cc_final: 0.8129 (p) REVERT: G 18 ASN cc_start: 0.8038 (m110) cc_final: 0.7832 (m110) REVERT: H 13 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7422 (tt0) REVERT: J 13 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7462 (tm-30) REVERT: F 11 MET cc_start: 0.8326 (pmm) cc_final: 0.7794 (pmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0949 time to fit residues: 12.0345 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 : 0.632 ------------------------------------------------------------------------------- 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: 3.9990 chunk 94 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 159 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS C 15 GLN I 18 ASN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 405 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.089216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.057630 restraints weight = 66463.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059518 restraints weight = 38074.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.060738 restraints weight = 27525.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061493 restraints weight = 22757.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.061836 restraints weight = 20358.125| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3550 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= 0.111 Angle : 0.628 10.268 20786 Z= 0.314 Chirality : 0.047 0.439 2320 Planarity : 0.003 0.042 2632 Dihedral : 5.085 35.076 1976 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.63 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: -1.43 (0.21), residues: 1770 helix: -0.10 (0.32), residues: 282 sheet: -0.56 (0.28), residues: 320 loop : -1.33 (0.20), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 873 TYR 0.047 0.001 TYR C 19 PHE 0.014 0.001 PHE E 427 TRP 0.012 0.001 TRP F 559 HIS 0.005 0.001 HIS F 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15218) covalent geometry : angle 0.60659 / 0.31 (20630) SS BOND : bond 0.00291 / 0.22 ( 48) SS BOND : angle 1.06080 / 0.70 ( 96) hydrogen bonds : bond 0.03534 / 2.21 ( 346) hydrogen bonds : angle 5.62170 / 3.80 ( 954) link_NAG-ASN : bond 0.00419 / 0.28 ( 20) link_NAG-ASN : angle 2.90129 / 2.07 ( 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 80 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.586 Fit side-chains REVERT: H 13 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7364 (tt0) REVERT: J 13 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7442 (tm-30) REVERT: J 17 LEU cc_start: 0.6618 (mt) cc_final: 0.6285 (mt) REVERT: F 11 MET cc_start: 0.8326 (pmm) cc_final: 0.7839 (pmm) REVERT: F 806 MET cc_start: 0.8223 (ptp) cc_final: 0.7932 (mpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0955 time to fit residues: 13.2184 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 : 0.597 ------------------------------------------------------------------------------- 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: 0.8980 chunk 105 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN ** E 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** 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 = 0.3919 r_free = 0.3919 target = 0.088994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057626 restraints weight = 66539.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059273 restraints weight = 40294.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.060388 restraints weight = 30163.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061039 restraints weight = 25369.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061509 restraints weight = 22922.751| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15286 Z= 0.122 Angle : 0.624 10.810 20786 Z= 0.310 Chirality : 0.047 0.322 2320 Planarity : 0.003 0.042 2632 Dihedral : 5.013 37.996 1976 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.91 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 (0.21), residues: 1770 helix: 0.15 (0.32), residues: 274 sheet: -0.44 (0.29), residues: 310 loop : -1.37 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 804 TYR 0.039 0.001 TYR A 19 PHE 0.010 0.001 PHE F 705 TRP 0.010 0.001 TRP E 414 HIS 0.005 0.001 HIS F 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15218) covalent geometry : angle 0.59809 / 0.30 (20630) SS BOND : bond 0.00237 / 0.15 ( 48) SS BOND : angle 1.03233 / 0.69 ( 96) hydrogen bonds : bond 0.03419 / 2.13 ( 346) hydrogen bonds : angle 5.56505 / 3.77 ( 954) link_NAG-ASN : bond 0.00401 / 0.26 ( 20) link_NAG-ASN : angle 3.19574 / 2.26 ( 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 74 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: H 13 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7399 (tt0) REVERT: J 13 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7323 (tm-30) REVERT: J 17 LEU cc_start: 0.6540 (mt) cc_final: 0.6192 (mt) REVERT: F 11 MET cc_start: 0.8334 (pmm) cc_final: 0.7854 (pmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0931 time to fit residues: 11.9507 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 : 0.592 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.088199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056400 restraints weight = 66609.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057992 restraints weight = 41236.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.059060 restraints weight = 31136.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059693 restraints weight = 26372.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059929 restraints weight = 23929.989| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15286 Z= 0.183 Angle : 0.663 11.047 20786 Z= 0.329 Chirality : 0.047 0.287 2320 Planarity : 0.004 0.043 2632 Dihedral : 5.134 39.567 1976 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.10 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -1.33 (0.21), residues: 1770 helix: 0.33 (0.33), residues: 264 sheet: -0.56 (0.28), residues: 320 loop : -1.31 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 774 TYR 0.013 0.001 TYR F 91 PHE 0.015 0.001 PHE E 572 TRP 0.010 0.001 TRP E 414 HIS 0.005 0.001 HIS F 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (15218) covalent geometry : angle 0.64029 / 0.32 (20630) SS BOND : bond 0.00274 / 0.18 ( 48) SS BOND : angle 1.08443 / 0.77 ( 96) hydrogen bonds : bond 0.03553 / 2.22 ( 346) hydrogen bonds : angle 5.65501 / 3.81 ( 954) link_NAG-ASN : bond 0.00435 / 0.26 ( 20) link_NAG-ASN : angle 3.10318 / 2.19 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2475.00 seconds wall clock time: 43 minutes 40.94 seconds (2620.94 seconds total)