Starting phenix.real_space_refine on Wed Mar 4 14:43:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8guy_34281/03_2026/8guy_34281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8guy_34281/03_2026/8guy_34281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8guy_34281/03_2026/8guy_34281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8guy_34281/03_2026/8guy_34281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8guy_34281/03_2026/8guy_34281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8guy_34281/03_2026/8guy_34281.map" } resolution = 4.18 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= 0.048 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 114 5.16 5 C 9006 2.51 5 N 2456 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14222 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 6736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 bond proxies already assigned to first conformer: 6887 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "C" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Conformer: "B" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} bond proxies already assigned to first conformer: 191 Chain: "F" Number of atoms: 6736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 835, 6729 Classifications: {'peptide': 835} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 787} Chain breaks: 3 bond proxies already assigned to first conformer: 6887 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR B 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 26 " occ=0.50 residue: pdb=" N ATYR D 26 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 26 " occ=0.50 Time building chain proxies: 5.39, per 1000 atoms: 0.38 Number of scatterers: 14222 At special positions: 0 Unit cell: (119.84, 132.68, 174.41, 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 114 16.00 O 2646 8.00 N 2456 7.00 C 9006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 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=2.04 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=2.02 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=2.04 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 524 " - pdb=" SG CYS F 524 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 683 " - pdb=" SG CYS F 683 " distance=2.04 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.04 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.04 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.02 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.02 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.02 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.04 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=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.04 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=2.04 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 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 32 sheets defined 15.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.923A pdb=" N GLU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.096A pdb=" N ILE E 131 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 137 removed outlier: 4.034A pdb=" N ILE E 136 " --> pdb=" O ASP E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.534A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU E 262 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS E 263 " --> pdb=" O CYS E 259 " (cutoff:3.500A) removed outlier: 3.866A 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 354 through 359 Processing helix chain 'E' and resid 413 through 417 removed outlier: 3.526A pdb=" N HIS E 417 " --> pdb=" O TRP E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 444 removed outlier: 3.851A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 644 removed outlier: 3.592A pdb=" N PHE E 642 " --> pdb=" O SER E 639 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU E 643 " --> pdb=" O GLU E 640 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 644 " --> pdb=" O LEU E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 714 removed outlier: 3.675A pdb=" N GLU E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN E 711 " --> pdb=" O ASP E 707 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 712 " --> pdb=" O TYR E 708 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 714 " --> pdb=" O HIS E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 813 Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.532A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.070A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.531A pdb=" N GLU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 10 through 19 removed outlier: 4.165A pdb=" N TYR D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 132 through 137 removed outlier: 4.021A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 152 removed outlier: 3.509A pdb=" N ASN F 152 " --> pdb=" O LYS F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.661A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU F 262 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' 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 354 through 359 Processing helix chain 'F' and resid 413 through 417 removed outlier: 3.510A pdb=" N HIS F 417 " --> pdb=" O TRP F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.877A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS F 440 " --> pdb=" O LEU F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 644 removed outlier: 3.530A pdb=" N PHE F 642 " --> pdb=" O SER F 639 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU F 643 " --> pdb=" O GLU F 640 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU F 644 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 714 removed outlier: 3.642A pdb=" N GLU F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR F 708 " --> pdb=" O THR F 704 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 711 " --> pdb=" O ASP F 707 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 712 " --> pdb=" O TYR F 708 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 813 Processing helix chain 'F' and resid 862 through 870 Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 8 removed outlier: 6.954A pdb=" N GLU E 6 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE E 29 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N CYS E 8 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 82 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.832A pdb=" N MET E 11 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU E 36 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE E 13 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET E 38 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 64 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 37 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 66 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU E 61 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE E 96 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E 63 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLU E 120 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 95 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.362A pdb=" N ALA E 227 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN E 215 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N CYS E 225 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'E' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 312 removed outlier: 3.856A pdb=" N ILE E 364 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 318 through 321 removed outlier: 3.884A pdb=" N LYS E 319 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 341 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 472 through 473 Processing sheet with id=AB1, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AB2, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.678A pdb=" N ILE E 564 " --> pdb=" O ILE E 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 599 through 605 removed outlier: 5.491A pdb=" N ASP E 600 " --> pdb=" O LYS E 616 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS E 616 " --> pdb=" O ASP E 600 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 612 " --> pdb=" O VAL E 604 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 611 " --> pdb=" O ILE E 770 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 4.124A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 630 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 762 " --> pdb=" O TYR E 628 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS E 627 " --> pdb=" O CYS E 786 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 819 through 822 removed outlier: 3.543A pdb=" N VAL E 828 " --> pdb=" O LEU E 874 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 856 through 859 removed outlier: 3.548A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 886 " --> pdb=" O TRP E 897 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP E 897 " --> pdb=" O ILE E 886 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA E 888 " --> pdb=" O GLY E 895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 856 through 859 removed outlier: 3.548A pdb=" N VAL E 847 " --> pdb=" O LEU E 859 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 903 " --> pdb=" O TYR E 882 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 6 through 8 removed outlier: 6.954A pdb=" N GLU F 6 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE F 29 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS F 8 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 11 through 14 removed outlier: 3.658A pdb=" N PHE F 64 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 37 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU F 61 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N PHE F 96 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU F 63 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N GLU F 120 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE F 95 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.237A pdb=" N ALA F 227 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASN F 215 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N CYS F 225 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AC3, first strand: chain 'F' and resid 278 through 280 Processing sheet with id=AC4, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AC5, first strand: chain 'F' and resid 311 through 312 removed outlier: 3.801A pdb=" N ILE F 364 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 318 through 321 removed outlier: 3.777A pdb=" N LYS F 319 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE F 341 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG F 371 " --> pdb=" O ILE F 342 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=AC8, first strand: chain 'F' and resid 475 through 480 Processing sheet with id=AC9, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.530A pdb=" N LYS F 508 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 564 " --> pdb=" O ILE F 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 599 through 605 removed outlier: 5.430A pdb=" N ASP F 600 " --> pdb=" O LYS F 616 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS F 616 " --> pdb=" O ASP F 600 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE F 612 " --> pdb=" O VAL F 604 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 611 " --> pdb=" O ILE F 770 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 761 through 762 removed outlier: 3.680A pdb=" N VAL F 762 " --> pdb=" O TYR F 628 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS F 627 " --> pdb=" O CYS F 786 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 819 through 822 removed outlier: 3.545A pdb=" N VAL F 828 " --> pdb=" O LEU F 874 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 857 through 859 removed outlier: 3.586A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 886 " --> pdb=" O TRP F 897 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TRP F 897 " --> pdb=" O ILE F 886 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA F 888 " --> pdb=" O GLY F 895 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 857 through 859 removed outlier: 3.586A pdb=" N VAL F 847 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 903 " --> pdb=" O TYR F 882 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 789 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: 2.74 Time building geometry restraints manager: 1.66 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: 4683 1.35 - 1.48: 3636 1.48 - 1.60: 6121 1.60 - 1.73: 0 1.73 - 1.85: 136 Bond restraints: 14576 Sorted by residual: bond pdb=" CB GLU F 637 " pdb=" CG GLU F 637 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.21e+00 bond pdb=" CB CYS F 435 " pdb=" SG CYS F 435 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CB GLU E 637 " pdb=" CG GLU E 637 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB CYS E 435 " pdb=" SG CYS E 435 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.73e+00 bond pdb=" CA THR E 578 " pdb=" CB THR E 578 " ideal model delta sigma weight residual 1.527 1.553 -0.026 1.61e-02 3.86e+03 2.51e+00 ... (remaining 14571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 18992 2.32 - 4.63: 652 4.63 - 6.95: 97 6.95 - 9.27: 23 9.27 - 11.59: 6 Bond angle restraints: 19770 Sorted by residual: angle pdb=" N VAL E 445 " pdb=" CA VAL E 445 " pdb=" C VAL E 445 " ideal model delta sigma weight residual 112.96 105.76 7.20 1.00e+00 1.00e+00 5.18e+01 angle pdb=" C ARG E 577 " pdb=" N THR E 578 " pdb=" CA THR E 578 " ideal model delta sigma weight residual 122.82 128.40 -5.58 1.42e+00 4.96e-01 1.54e+01 angle pdb=" C ARG F 14 " pdb=" N ASN F 15 " pdb=" CA ASN F 15 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N GLU E 808 " pdb=" CA GLU E 808 " pdb=" C GLU E 808 " ideal model delta sigma weight residual 110.53 115.59 -5.06 1.32e+00 5.74e-01 1.47e+01 angle pdb=" CA CYS F 308 " pdb=" CB CYS F 308 " pdb=" SG CYS F 308 " ideal model delta sigma weight residual 114.40 123.19 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 19765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7845 17.90 - 35.80: 830 35.80 - 53.70: 130 53.70 - 71.60: 47 71.60 - 89.51: 16 Dihedral angle restraints: 8868 sinusoidal: 3704 harmonic: 5164 Sorted by residual: dihedral pdb=" CA PRO E 243 " pdb=" C PRO E 243 " pdb=" N PRO E 244 " pdb=" CA PRO E 244 " ideal model delta harmonic sigma weight residual 180.00 133.72 46.28 0 5.00e+00 4.00e-02 8.57e+01 dihedral pdb=" CB CYS F 647 " pdb=" SG CYS F 647 " pdb=" SG CYS F 860 " pdb=" CB CYS F 860 " ideal model delta sinusoidal sigma weight residual 93.00 176.28 -83.28 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CA PRO F 243 " pdb=" C PRO F 243 " pdb=" N PRO F 244 " pdb=" CA PRO F 244 " ideal model delta harmonic sigma weight residual 180.00 134.03 45.97 0 5.00e+00 4.00e-02 8.45e+01 ... (remaining 8865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1654 0.065 - 0.131: 403 0.131 - 0.196: 67 0.196 - 0.262: 15 0.262 - 0.327: 1 Chirality restraints: 2140 Sorted by residual: chirality pdb=" CB THR F 790 " pdb=" CA THR F 790 " pdb=" OG1 THR F 790 " pdb=" CG2 THR F 790 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA THR F 790 " pdb=" N THR F 790 " pdb=" C THR F 790 " pdb=" CB THR F 790 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE E 781 " pdb=" CA ILE E 781 " pdb=" CG1 ILE E 781 " pdb=" CG2 ILE E 781 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2137 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 243 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO F 244 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO F 244 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO F 244 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 243 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO E 244 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO E 244 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 244 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 242 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO F 243 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F 243 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 243 " 0.047 5.00e-02 4.00e+02 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2977 2.78 - 3.31: 12547 3.31 - 3.84: 23562 3.84 - 4.37: 25822 4.37 - 4.90: 43345 Nonbonded interactions: 108253 Sorted by model distance: nonbonded pdb=" OD1 ASP E 59 " pdb=" OG SER E 85 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP F 59 " pdb=" OG SER F 85 " model vdw 2.258 3.040 nonbonded pdb=" OG SER E 116 " pdb=" OD1 ASN E 143 " model vdw 2.299 3.040 nonbonded pdb=" OG SER F 116 " pdb=" OD1 ASN F 143 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR F 334 " pdb=" OE1 GLU F 362 " model vdw 2.333 3.040 ... (remaining 108248 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 3 through 25 or resid 27)) selection = (chain 'D' and (resid 3 through 25 or resid 27)) } ncs_group { reference = (chain 'E' and (resid 1 through 143 or resid 145 through 907)) selection = (chain 'F' and (resid 1 through 143 or resid 145 through 907)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.700 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14620 Z= 0.243 Angle : 1.017 11.587 19858 Z= 0.544 Chirality : 0.060 0.327 2140 Planarity : 0.007 0.112 2566 Dihedral : 14.547 89.506 5408 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % Twisted General : 0.12 % 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: -4.23 (0.17), residues: 1744 helix: -4.43 (0.16), residues: 216 sheet: -1.99 (0.27), residues: 316 loop : -2.92 (0.15), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 774 TYR 0.018 0.002 TYR F 708 PHE 0.021 0.002 PHE E 776 TRP 0.021 0.002 TRP F 412 HIS 0.007 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00511 (14576) covalent geometry : angle 1.00498 (19770) SS BOND : bond 0.00608 ( 44) SS BOND : angle 2.51315 ( 88) hydrogen bonds : bond 0.33485 ( 291) hydrogen bonds : angle 10.67611 ( 789) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8459 (tp) cc_final: 0.8086 (tp) REVERT: E 405 ASN cc_start: 0.8688 (m-40) cc_final: 0.8431 (m110) REVERT: E 439 ILE cc_start: 0.9224 (pt) cc_final: 0.8977 (mt) REVERT: E 442 MET cc_start: 0.9351 (tpt) cc_final: 0.8902 (tpt) REVERT: E 698 GLU cc_start: 0.7758 (pp20) cc_final: 0.7524 (tm-30) REVERT: A 2 ILE cc_start: 0.9529 (tt) cc_final: 0.9317 (tt) REVERT: C 17 GLU cc_start: 0.8504 (pp20) cc_final: 0.8073 (pp20) REVERT: F 439 ILE cc_start: 0.8987 (pt) cc_final: 0.8698 (mt) REVERT: F 442 MET cc_start: 0.9295 (tpt) cc_final: 0.9005 (tpt) REVERT: F 698 GLU cc_start: 0.8177 (pp20) cc_final: 0.7891 (tm-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1079 time to fit residues: 23.1848 Evaluate side-chains 79 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN E 249 GLN E 282 ASN E 589 GLN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 627 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 HIS F 32 HIS F 177 GLN F 187 HIS F 249 GLN F 431 ASN F 589 GLN F 622 ASN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.091097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.062981 restraints weight = 245172.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.065267 restraints weight = 102912.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.066403 restraints weight = 54185.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.066451 restraints weight = 41256.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.067252 restraints weight = 36938.903| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14620 Z= 0.162 Angle : 0.715 6.768 19858 Z= 0.375 Chirality : 0.047 0.193 2140 Planarity : 0.006 0.101 2566 Dihedral : 6.561 76.354 1938 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 0.25 % Allowed : 3.36 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -3.46 (0.18), residues: 1744 helix: -3.22 (0.25), residues: 190 sheet: -1.80 (0.28), residues: 306 loop : -2.44 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 717 TYR 0.014 0.001 TYR E 708 PHE 0.018 0.002 PHE E 497 TRP 0.016 0.001 TRP F 412 HIS 0.005 0.001 HIS E 858 Details of bonding type rmsd covalent geometry : bond 0.00360 (14576) covalent geometry : angle 0.70412 (19770) SS BOND : bond 0.00353 ( 44) SS BOND : angle 1.97120 ( 88) hydrogen bonds : bond 0.05501 ( 291) hydrogen bonds : angle 7.21233 ( 789) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7974 (tp) cc_final: 0.7029 (tp) REVERT: E 57 ILE cc_start: 0.9066 (mt) cc_final: 0.8688 (mt) REVERT: E 314 LEU cc_start: 0.9381 (tp) cc_final: 0.9166 (tt) REVERT: E 572 PHE cc_start: 0.7598 (t80) cc_final: 0.7345 (t80) REVERT: E 613 LEU cc_start: 0.8664 (tp) cc_final: 0.8444 (pp) REVERT: D 6 LEU cc_start: 0.9269 (mt) cc_final: 0.9037 (mt) REVERT: F 405 ASN cc_start: 0.8369 (m-40) cc_final: 0.8072 (p0) REVERT: F 707 ASP cc_start: 0.9069 (m-30) cc_final: 0.8741 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0946 time to fit residues: 17.3440 Evaluate side-chains 69 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 51 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 81 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 787 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.091396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.065805 restraints weight = 205731.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.065254 restraints weight = 104032.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067074 restraints weight = 63071.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067456 restraints weight = 41176.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.068271 restraints weight = 36157.437| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14620 Z= 0.131 Angle : 0.654 8.268 19858 Z= 0.340 Chirality : 0.046 0.192 2140 Planarity : 0.005 0.103 2566 Dihedral : 6.136 83.260 1938 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.25 % Allowed : 2.55 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -3.05 (0.19), residues: 1744 helix: -2.34 (0.32), residues: 182 sheet: -1.76 (0.26), residues: 364 loop : -2.17 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 702 TYR 0.013 0.001 TYR E 401 PHE 0.019 0.002 PHE F 427 TRP 0.013 0.001 TRP F 412 HIS 0.004 0.000 HIS F 429 Details of bonding type rmsd covalent geometry : bond 0.00301 (14576) covalent geometry : angle 0.64739 (19770) SS BOND : bond 0.00332 ( 44) SS BOND : angle 1.56126 ( 88) hydrogen bonds : bond 0.04465 ( 291) hydrogen bonds : angle 6.46848 ( 789) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8013 (tp) cc_final: 0.7129 (tp) REVERT: E 405 ASN cc_start: 0.8852 (m-40) cc_final: 0.8543 (m110) REVERT: E 442 MET cc_start: 0.9294 (tpt) cc_final: 0.8975 (tpt) REVERT: E 504 MET cc_start: 0.8287 (mtp) cc_final: 0.8058 (mtm) REVERT: D 6 LEU cc_start: 0.9241 (mt) cc_final: 0.9039 (mt) REVERT: F 36 LEU cc_start: 0.8312 (tp) cc_final: 0.8034 (tp) REVERT: F 333 CYS cc_start: 0.6154 (p) cc_final: 0.5912 (p) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0933 time to fit residues: 15.6373 Evaluate side-chains 67 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 152 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 527 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS ** F 627 HIS ** 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 = 0.3890 r_free = 0.3890 target = 0.090640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061705 restraints weight = 183874.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.063497 restraints weight = 89795.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064431 restraints weight = 53943.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064963 restraints weight = 39194.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065592 restraints weight = 36090.699| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14620 Z= 0.149 Angle : 0.644 6.829 19858 Z= 0.332 Chirality : 0.046 0.187 2140 Planarity : 0.005 0.105 2566 Dihedral : 5.976 83.275 1938 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.25 % Allowed : 2.12 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.82 (0.20), residues: 1744 helix: -1.67 (0.35), residues: 194 sheet: -1.56 (0.26), residues: 350 loop : -2.12 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 135 TYR 0.012 0.001 TYR E 60 PHE 0.024 0.002 PHE E 572 TRP 0.031 0.002 TRP E 529 HIS 0.004 0.001 HIS F 429 Details of bonding type rmsd covalent geometry : bond 0.00347 (14576) covalent geometry : angle 0.63863 (19770) SS BOND : bond 0.00286 ( 44) SS BOND : angle 1.41738 ( 88) hydrogen bonds : bond 0.03890 ( 291) hydrogen bonds : angle 6.13799 ( 789) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.8084 (tp) cc_final: 0.7332 (tp) REVERT: E 405 ASN cc_start: 0.9019 (m-40) cc_final: 0.8687 (m110) REVERT: E 504 MET cc_start: 0.8355 (mtp) cc_final: 0.8092 (mtm) REVERT: A 14 TYR cc_start: 0.7969 (t80) cc_final: 0.7340 (t80) REVERT: A 17 GLU cc_start: 0.8552 (pp20) cc_final: 0.8074 (pp20) REVERT: D 6 LEU cc_start: 0.9137 (mt) cc_final: 0.8923 (mt) REVERT: F 36 LEU cc_start: 0.8212 (tp) cc_final: 0.7927 (tp) REVERT: F 405 ASN cc_start: 0.8855 (m-40) cc_final: 0.8543 (m110) REVERT: F 442 MET cc_start: 0.9236 (tpt) cc_final: 0.8959 (tpt) REVERT: F 832 TRP cc_start: 0.6371 (p90) cc_final: 0.6120 (p-90) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1168 time to fit residues: 16.1709 Evaluate side-chains 64 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 99 optimal weight: 0.4980 chunk 169 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 58 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 overall best weight: 2.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 HIS ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 423 GLN ** F 627 HIS ** 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 = 0.3842 r_free = 0.3842 target = 0.088907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.060774 restraints weight = 224619.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061278 restraints weight = 99670.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062783 restraints weight = 63822.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063360 restraints weight = 44039.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.063953 restraints weight = 39300.362| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14620 Z= 0.199 Angle : 0.686 7.300 19858 Z= 0.352 Chirality : 0.047 0.189 2140 Planarity : 0.005 0.105 2566 Dihedral : 6.013 80.683 1938 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 0.25 % Allowed : 1.87 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.71 (0.20), residues: 1744 helix: -1.37 (0.36), residues: 196 sheet: -1.38 (0.28), residues: 320 loop : -2.13 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 14 TYR 0.015 0.001 TYR E 60 PHE 0.030 0.002 PHE F 382 TRP 0.018 0.001 TRP F 412 HIS 0.006 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00457 (14576) covalent geometry : angle 0.67773 (19770) SS BOND : bond 0.00311 ( 44) SS BOND : angle 1.69709 ( 88) hydrogen bonds : bond 0.04061 ( 291) hydrogen bonds : angle 6.00774 ( 789) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7934 (tp) cc_final: 0.6995 (tp) REVERT: E 405 ASN cc_start: 0.9020 (m-40) cc_final: 0.8708 (m110) REVERT: E 442 MET cc_start: 0.9284 (tpt) cc_final: 0.8869 (tpt) REVERT: E 504 MET cc_start: 0.8417 (mtp) cc_final: 0.8166 (mtm) REVERT: A 14 TYR cc_start: 0.8028 (t80) cc_final: 0.7370 (t80) REVERT: A 17 GLU cc_start: 0.8633 (pp20) cc_final: 0.8274 (pp20) REVERT: C 14 TYR cc_start: 0.7857 (t80) cc_final: 0.6997 (t80) REVERT: F 36 LEU cc_start: 0.8333 (tp) cc_final: 0.8132 (tp) REVERT: F 405 ASN cc_start: 0.8922 (m-40) cc_final: 0.8662 (m110) REVERT: F 442 MET cc_start: 0.9246 (tpt) cc_final: 0.8928 (tpt) REVERT: F 504 MET cc_start: 0.8444 (mtp) cc_final: 0.8126 (mtm) REVERT: F 602 ILE cc_start: 0.9060 (mm) cc_final: 0.8719 (mm) REVERT: F 614 LYS cc_start: 0.9393 (ptpp) cc_final: 0.9132 (ptmm) REVERT: F 832 TRP cc_start: 0.6514 (p90) cc_final: 0.6244 (p-90) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1126 time to fit residues: 15.1118 Evaluate side-chains 60 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 156 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 HIS ** F 627 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.090038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.063300 restraints weight = 209268.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.063340 restraints weight = 104724.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065125 restraints weight = 63025.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065239 restraints weight = 42343.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066186 restraints weight = 38351.914| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14620 Z= 0.119 Angle : 0.621 6.797 19858 Z= 0.317 Chirality : 0.045 0.183 2140 Planarity : 0.005 0.108 2566 Dihedral : 5.706 80.972 1938 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.25 % Allowed : 0.93 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.51 (0.20), residues: 1744 helix: -1.21 (0.38), residues: 194 sheet: -1.35 (0.27), residues: 350 loop : -1.95 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 702 TYR 0.011 0.001 TYR E 401 PHE 0.015 0.001 PHE E 497 TRP 0.017 0.001 TRP E 412 HIS 0.003 0.000 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00278 (14576) covalent geometry : angle 0.61492 (19770) SS BOND : bond 0.00231 ( 44) SS BOND : angle 1.40711 ( 88) hydrogen bonds : bond 0.03502 ( 291) hydrogen bonds : angle 5.72263 ( 789) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7777 (tp) cc_final: 0.6931 (tp) REVERT: E 262 LEU cc_start: 0.9182 (mt) cc_final: 0.8637 (mt) REVERT: E 294 MET cc_start: 0.8454 (ppp) cc_final: 0.7904 (tpp) REVERT: E 333 CYS cc_start: 0.6589 (p) cc_final: 0.6375 (p) REVERT: E 405 ASN cc_start: 0.8824 (m-40) cc_final: 0.8472 (m110) REVERT: E 504 MET cc_start: 0.8414 (mtp) cc_final: 0.8123 (mtm) REVERT: A 14 TYR cc_start: 0.8013 (t80) cc_final: 0.7379 (t80) REVERT: A 17 GLU cc_start: 0.8583 (pp20) cc_final: 0.8199 (pp20) REVERT: B 6 LEU cc_start: 0.9164 (mt) cc_final: 0.8883 (mt) REVERT: C 14 TYR cc_start: 0.7866 (t80) cc_final: 0.7340 (t80) REVERT: C 17 GLU cc_start: 0.8478 (pp20) cc_final: 0.8155 (pp20) REVERT: F 405 ASN cc_start: 0.8778 (m-40) cc_final: 0.8489 (m-40) REVERT: F 442 MET cc_start: 0.9099 (tpt) cc_final: 0.8848 (tpt) REVERT: F 504 MET cc_start: 0.8361 (mtp) cc_final: 0.8045 (mtm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0969 time to fit residues: 14.1526 Evaluate side-chains 68 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 527 ASN ** F 627 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.088682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.062176 restraints weight = 210368.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061789 restraints weight = 111002.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.063583 restraints weight = 63925.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.063678 restraints weight = 40638.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.065871 restraints weight = 38703.924| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14620 Z= 0.178 Angle : 0.656 7.218 19858 Z= 0.334 Chirality : 0.046 0.179 2140 Planarity : 0.005 0.107 2566 Dihedral : 5.728 79.517 1938 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.25 % Allowed : 0.68 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.43 (0.20), residues: 1744 helix: -0.94 (0.39), residues: 178 sheet: -1.27 (0.28), residues: 330 loop : -1.94 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 331 TYR 0.013 0.001 TYR E 60 PHE 0.014 0.002 PHE D 24 TRP 0.016 0.001 TRP F 412 HIS 0.003 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00409 (14576) covalent geometry : angle 0.65064 (19770) SS BOND : bond 0.00286 ( 44) SS BOND : angle 1.43499 ( 88) hydrogen bonds : bond 0.03745 ( 291) hydrogen bonds : angle 5.76112 ( 789) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7803 (tp) cc_final: 0.6928 (tp) REVERT: E 262 LEU cc_start: 0.9048 (mt) cc_final: 0.8833 (mt) REVERT: E 333 CYS cc_start: 0.6566 (p) cc_final: 0.6260 (p) REVERT: E 405 ASN cc_start: 0.8996 (m-40) cc_final: 0.8763 (m110) REVERT: E 442 MET cc_start: 0.9292 (tpt) cc_final: 0.8776 (tpt) REVERT: E 504 MET cc_start: 0.8418 (mtp) cc_final: 0.8185 (mtm) REVERT: A 14 TYR cc_start: 0.7945 (t80) cc_final: 0.7378 (t80) REVERT: A 17 GLU cc_start: 0.8518 (pp20) cc_final: 0.8234 (pp20) REVERT: F 256 PHE cc_start: 0.9355 (p90) cc_final: 0.9142 (p90) REVERT: F 442 MET cc_start: 0.9134 (tpt) cc_final: 0.8907 (tpt) REVERT: F 504 MET cc_start: 0.8414 (mtp) cc_final: 0.8135 (mtm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0994 time to fit residues: 14.0735 Evaluate side-chains 62 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 168 optimal weight: 10.0000 chunk 44 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 chunk 68 optimal weight: 1.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.088809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.061027 restraints weight = 218215.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.061572 restraints weight = 100769.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062415 restraints weight = 61806.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062822 restraints weight = 43454.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063565 restraints weight = 37185.799| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14620 Z= 0.159 Angle : 0.635 7.032 19858 Z= 0.324 Chirality : 0.045 0.171 2140 Planarity : 0.005 0.109 2566 Dihedral : 5.666 79.537 1938 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.25 % Allowed : 0.81 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.44 (0.20), residues: 1744 helix: -1.18 (0.38), residues: 194 sheet: -1.26 (0.28), residues: 330 loop : -1.91 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 252 TYR 0.012 0.001 TYR E 60 PHE 0.027 0.001 PHE E 497 TRP 0.018 0.001 TRP E 251 HIS 0.003 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00367 (14576) covalent geometry : angle 0.62950 (19770) SS BOND : bond 0.00379 ( 44) SS BOND : angle 1.38209 ( 88) hydrogen bonds : bond 0.03549 ( 291) hydrogen bonds : angle 5.72407 ( 789) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7807 (tp) cc_final: 0.6958 (tp) REVERT: E 262 LEU cc_start: 0.9044 (mt) cc_final: 0.8839 (mt) REVERT: E 294 MET cc_start: 0.8393 (ppp) cc_final: 0.7853 (tpp) REVERT: E 333 CYS cc_start: 0.6863 (p) cc_final: 0.6533 (p) REVERT: E 405 ASN cc_start: 0.8914 (m-40) cc_final: 0.8617 (m110) REVERT: E 442 MET cc_start: 0.9231 (tpt) cc_final: 0.8673 (tpt) REVERT: E 504 MET cc_start: 0.8417 (mtp) cc_final: 0.8159 (mtm) REVERT: A 14 TYR cc_start: 0.8102 (t80) cc_final: 0.7549 (t80) REVERT: A 17 GLU cc_start: 0.8664 (pp20) cc_final: 0.8336 (pp20) REVERT: F 256 PHE cc_start: 0.9380 (p90) cc_final: 0.9159 (p90) REVERT: F 405 ASN cc_start: 0.8938 (m-40) cc_final: 0.8605 (m110) REVERT: F 442 MET cc_start: 0.9088 (tpt) cc_final: 0.8870 (tpt) REVERT: F 504 MET cc_start: 0.8416 (mtp) cc_final: 0.8136 (mtm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0901 time to fit residues: 12.5996 Evaluate side-chains 63 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 148 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 165 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.089296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.060507 restraints weight = 170530.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060766 restraints weight = 88710.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062773 restraints weight = 54980.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062253 restraints weight = 41109.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.063097 restraints weight = 37907.786| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14620 Z= 0.130 Angle : 0.612 7.334 19858 Z= 0.311 Chirality : 0.045 0.173 2140 Planarity : 0.005 0.109 2566 Dihedral : 5.516 79.042 1938 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.25 % Allowed : 0.12 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.36 (0.20), residues: 1744 helix: -1.06 (0.38), residues: 194 sheet: -1.22 (0.29), residues: 314 loop : -1.86 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 498 TYR 0.018 0.001 TYR C 14 PHE 0.027 0.001 PHE E 497 TRP 0.020 0.001 TRP E 251 HIS 0.002 0.000 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00306 (14576) covalent geometry : angle 0.60647 (19770) SS BOND : bond 0.00252 ( 44) SS BOND : angle 1.34283 ( 88) hydrogen bonds : bond 0.03420 ( 291) hydrogen bonds : angle 5.63614 ( 789) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7869 (tp) cc_final: 0.7012 (tp) REVERT: E 262 LEU cc_start: 0.9057 (mt) cc_final: 0.8816 (mt) REVERT: E 294 MET cc_start: 0.8428 (ppp) cc_final: 0.7866 (tpp) REVERT: E 333 CYS cc_start: 0.6806 (p) cc_final: 0.6469 (p) REVERT: E 405 ASN cc_start: 0.9083 (m-40) cc_final: 0.8597 (m110) REVERT: E 442 MET cc_start: 0.9220 (tpt) cc_final: 0.8666 (tpt) REVERT: E 504 MET cc_start: 0.8448 (mtp) cc_final: 0.8098 (mtm) REVERT: A 14 TYR cc_start: 0.8090 (t80) cc_final: 0.7535 (t80) REVERT: A 17 GLU cc_start: 0.8623 (pp20) cc_final: 0.8250 (pp20) REVERT: B 6 LEU cc_start: 0.9150 (mt) cc_final: 0.8864 (mt) REVERT: D 6 LEU cc_start: 0.9202 (mt) cc_final: 0.8953 (mt) REVERT: F 56 MET cc_start: 0.8177 (tpp) cc_final: 0.7969 (tpt) REVERT: F 256 PHE cc_start: 0.9372 (p90) cc_final: 0.9172 (p90) REVERT: F 405 ASN cc_start: 0.9043 (m-40) cc_final: 0.8551 (m110) REVERT: F 504 MET cc_start: 0.8530 (mtp) cc_final: 0.8226 (mtm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0898 time to fit residues: 12.7035 Evaluate side-chains 65 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 57 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 521 GLN E 547 ASN ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.087626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061154 restraints weight = 204660.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060867 restraints weight = 107087.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.062939 restraints weight = 65474.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.062478 restraints weight = 47535.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.063912 restraints weight = 41901.418| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14620 Z= 0.272 Angle : 0.749 9.110 19858 Z= 0.380 Chirality : 0.048 0.171 2140 Planarity : 0.006 0.107 2566 Dihedral : 6.005 78.494 1938 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 0.25 % Allowed : 0.12 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.66 (0.20), residues: 1744 helix: -1.32 (0.36), residues: 194 sheet: -1.45 (0.28), residues: 312 loop : -2.06 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 539 TYR 0.021 0.002 TYR F 60 PHE 0.031 0.002 PHE E 497 TRP 0.028 0.002 TRP E 251 HIS 0.004 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00628 (14576) covalent geometry : angle 0.74206 (19770) SS BOND : bond 0.00329 ( 44) SS BOND : angle 1.73358 ( 88) hydrogen bonds : bond 0.04200 ( 291) hydrogen bonds : angle 5.99529 ( 789) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 LEU cc_start: 0.7872 (tp) cc_final: 0.7015 (tp) REVERT: E 54 LEU cc_start: 0.9327 (tp) cc_final: 0.9052 (tt) REVERT: E 262 LEU cc_start: 0.9088 (mt) cc_final: 0.8872 (mt) REVERT: E 333 CYS cc_start: 0.6809 (p) cc_final: 0.6565 (p) REVERT: E 405 ASN cc_start: 0.8924 (m-40) cc_final: 0.8713 (m110) REVERT: E 504 MET cc_start: 0.8146 (mtp) cc_final: 0.7907 (mtm) REVERT: A 14 TYR cc_start: 0.8062 (t80) cc_final: 0.7788 (t80) REVERT: F 256 PHE cc_start: 0.9304 (p90) cc_final: 0.9102 (p90) REVERT: F 405 ASN cc_start: 0.8946 (m-40) cc_final: 0.8738 (m110) REVERT: F 442 MET cc_start: 0.9226 (tpt) cc_final: 0.9006 (tpt) REVERT: F 504 MET cc_start: 0.8152 (mtp) cc_final: 0.7929 (mtm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0907 time to fit residues: 11.9513 Evaluate side-chains 61 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.0370 chunk 68 optimal weight: 0.5980 chunk 119 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 47 optimal weight: 0.0570 chunk 97 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.090355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.063670 restraints weight = 195204.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064382 restraints weight = 93927.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.065427 restraints weight = 56297.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.065936 restraints weight = 37285.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.066535 restraints weight = 32856.506| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14620 Z= 0.103 Angle : 0.628 7.821 19858 Z= 0.316 Chirality : 0.045 0.175 2140 Planarity : 0.005 0.110 2566 Dihedral : 5.510 80.036 1938 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.25 % Allowed : 0.06 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 2.17 % 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: -2.30 (0.20), residues: 1744 helix: -1.06 (0.38), residues: 194 sheet: -1.14 (0.29), residues: 314 loop : -1.82 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 577 TYR 0.024 0.001 TYR F 512 PHE 0.028 0.001 PHE E 497 TRP 0.019 0.001 TRP F 412 HIS 0.003 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00238 (14576) covalent geometry : angle 0.62347 (19770) SS BOND : bond 0.00279 ( 44) SS BOND : angle 1.34183 ( 88) hydrogen bonds : bond 0.03304 ( 291) hydrogen bonds : angle 5.61980 ( 789) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.81 seconds wall clock time: 45 minutes 59.74 seconds (2759.74 seconds total)