Starting phenix.real_space_refine on Fri Mar 6 11:04:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sof_10273/03_2026/6sof_10273.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sof_10273/03_2026/6sof_10273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sof_10273/03_2026/6sof_10273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sof_10273/03_2026/6sof_10273.map" model { file = "/net/cci-nas-00/data/ceres_data/6sof_10273/03_2026/6sof_10273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sof_10273/03_2026/6sof_10273.cif" } resolution = 4.3 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= 0.154 sd= 1.821 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: 5 Type Number sf(0) Gaussians S 128 5.16 5 C 9966 2.51 5 N 2707 2.21 5 O 2968 1.98 5 H 14564 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30333 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 11127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 11127 Classifications: {'peptide': 719} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 678} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2532 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 152} Chain: "C" Number of atoms: 11118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 11118 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 40, 'TRANS': 678} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2508 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 9, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 286 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 471 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "E" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 299 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 471 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "K" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 292 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 471 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "I" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 292 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 466 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Time building chain proxies: 4.46, per 1000 atoms: 0.15 Number of scatterers: 30333 At special positions: 0 Unit cell: (118.72, 142.04, 166.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 O 2968 8.00 N 2707 7.00 C 9966 6.00 H 14564 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.04 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.02 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.05 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS C 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS B 860 " distance=2.04 Simple disulfide: pdb=" SG CYS A 682 " - pdb=" SG CYS A 685 " distance=2.03 Simple disulfide: pdb=" SG CYS A 683 " - pdb=" SG CYS C 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 795 " distance=2.02 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 26 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 182 " distance=2.02 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 216 " distance=2.04 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 241 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.02 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 435 " - pdb=" SG CYS C 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 647 " - pdb=" SG CYS D 860 " distance=2.03 Simple disulfide: pdb=" SG CYS C 682 " - pdb=" SG CYS C 685 " distance=2.03 Simple disulfide: pdb=" SG CYS D 786 " - pdb=" SG CYS D 795 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.04 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS F 19 " distance=2.04 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 11 " distance=2.04 Simple disulfide: pdb=" SG CYS K 7 " - pdb=" SG CYS L 7 " distance=2.03 Simple disulfide: pdb=" SG CYS K 20 " - pdb=" SG CYS L 19 " distance=2.03 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 11 " distance=2.05 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS J 7 " distance=2.04 Simple disulfide: pdb=" SG CYS I 20 " - pdb=" SG CYS J 19 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 826.4 milliseconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3700 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 30 sheets defined 15.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.654A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.117A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.610A pdb=" N ALA A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 445 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 689 through 691 No H-bonds generated for 'chain 'A' and resid 689 through 691' Processing helix chain 'A' and resid 692 through 714 removed outlier: 3.910A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'C' and resid 16 through 24 removed outlier: 3.559A pdb=" N ARG C 19 " --> pdb=" O ASN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.676A pdb=" N PHE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.803A pdb=" N LYS C 197 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.854A pdb=" N ILE C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 691 through 714 removed outlier: 3.741A pdb=" N GLU C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 813 removed outlier: 4.137A pdb=" N ASP D 812 " --> pdb=" O GLU D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 870 Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'H' and resid 8 through 20 removed outlier: 4.247A pdb=" N GLY H 20 " --> pdb=" O TYR H 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 12 through 18 Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'I' and resid 3 through 9 removed outlier: 3.714A pdb=" N SER I 9 " --> pdb=" O GLN I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 20 removed outlier: 3.639A pdb=" N LEU I 16 " --> pdb=" O SER I 12 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN I 18 " --> pdb=" O TYR I 14 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS I 20 " --> pdb=" O LEU I 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 4.006A pdb=" N VAL J 12 " --> pdb=" O GLY J 8 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 removed outlier: 9.488A pdb=" N VAL A 7 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 12.500A pdb=" N HIS A 32 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN A 34 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET A 11 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU A 36 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 9.488A pdb=" N VAL A 7 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 12.500A pdb=" N HIS A 32 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN A 34 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET A 11 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU A 36 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 65 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.609A pdb=" N THR A 172 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.507A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.894A pdb=" N PHE A 231 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.556A pdb=" N ILE A 388 " --> pdb=" O THR A 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 398 through 401 removed outlier: 7.792A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 477 through 480 Processing sheet with id=AB3, first strand: chain 'A' and resid 533 through 534 removed outlier: 3.953A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 605 removed outlier: 4.514A pdb=" N VAL A 604 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 612 " --> pdb=" O VAL A 604 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 760 through 762 removed outlier: 4.160A pdb=" N GLU B 760 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 630 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 762 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 628 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 13 removed outlier: 7.736A pdb=" N LEU C 61 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN C 34 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU C 63 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU C 36 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG C 65 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C 38 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.961A pdb=" N TYR C 144 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 212 through 216 removed outlier: 5.922A pdb=" N LEU C 213 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS C 228 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN C 215 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 245 through 247 Processing sheet with id=AC2, first strand: chain 'C' and resid 278 through 280 removed outlier: 3.519A pdb=" N ILE C 285 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 319 through 321 Processing sheet with id=AC4, first strand: chain 'C' and resid 335 through 336 removed outlier: 3.600A pdb=" N ILE C 364 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 402 through 403 removed outlier: 7.223A pdb=" N ALA C 402 " --> pdb=" O HIS C 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 471 through 472 removed outlier: 7.184A pdb=" N GLU C 471 " --> pdb=" O LYS C 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 475 through 480 removed outlier: 3.563A pdb=" N ARG C 479 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 533 through 534 removed outlier: 3.932A pdb=" N GLY C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 602 through 604 removed outlier: 3.721A pdb=" N LYS C 614 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 611 " --> pdb=" O ILE D 770 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 770 " --> pdb=" O ILE C 611 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 779 through 780 removed outlier: 3.712A pdb=" N TYR D 779 " --> pdb=" O ALA D 803 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 820 through 823 removed outlier: 3.644A pdb=" N VAL D 827 " --> pdb=" O PHE D 823 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 880 through 884 removed outlier: 3.875A pdb=" N VAL D 884 " --> pdb=" O THR D 901 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR D 901 " --> pdb=" O VAL D 884 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 663 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: 6.19 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14562 1.03 - 1.24: 2059 1.24 - 1.44: 5035 1.44 - 1.65: 8915 1.65 - 1.85: 150 Bond restraints: 30721 Sorted by residual: bond pdb=" CB CYS B 786 " pdb=" SG CYS B 786 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.26e+00 bond pdb=" C VAL B 911 " pdb=" N PRO B 912 " ideal model delta sigma weight residual 1.339 1.399 -0.059 3.40e-02 8.65e+02 3.05e+00 bond pdb=" CG ARG A 577 " pdb=" CD ARG A 577 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CB ASN C 337 " pdb=" CG ASN C 337 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.34e+00 bond pdb=" N ILE G 10 " pdb=" CA ILE G 10 " ideal model delta sigma weight residual 1.474 1.451 0.024 1.57e-02 4.06e+03 2.29e+00 ... (remaining 30716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.74: 55163 7.74 - 15.48: 4 15.48 - 23.21: 0 23.21 - 30.95: 1 30.95 - 38.69: 5 Bond angle restraints: 55173 Sorted by residual: angle pdb=" C GLN C 276 " pdb=" CA GLN C 276 " pdb=" HA GLN C 276 " ideal model delta sigma weight residual 109.00 70.31 38.69 3.00e+00 1.11e-01 1.66e+02 angle pdb=" CB CYS C 288 " pdb=" CA CYS C 288 " pdb=" HA CYS C 288 " ideal model delta sigma weight residual 109.00 71.81 37.19 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C CYS C 288 " pdb=" CA CYS C 288 " pdb=" HA CYS C 288 " ideal model delta sigma weight residual 109.00 73.02 35.98 3.00e+00 1.11e-01 1.44e+02 angle pdb=" N GLN C 276 " pdb=" CA GLN C 276 " pdb=" HA GLN C 276 " ideal model delta sigma weight residual 110.00 75.10 34.90 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N CYS C 288 " pdb=" CA CYS C 288 " pdb=" HA CYS C 288 " ideal model delta sigma weight residual 110.00 75.62 34.38 3.00e+00 1.11e-01 1.31e+02 ... (remaining 55168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13001 17.91 - 35.83: 1324 35.83 - 53.74: 393 53.74 - 71.66: 114 71.66 - 89.57: 39 Dihedral angle restraints: 14871 sinusoidal: 7971 harmonic: 6900 Sorted by residual: dihedral pdb=" CB CYS I 6 " pdb=" SG CYS I 6 " pdb=" SG CYS I 11 " pdb=" CB CYS I 11 " ideal model delta sinusoidal sigma weight residual -86.00 0.66 -86.66 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS E 7 " pdb=" SG CYS E 7 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -170.30 84.30 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual 93.00 10.56 82.44 1 1.00e+01 1.00e-02 8.34e+01 ... (remaining 14868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1886 0.059 - 0.119: 407 0.119 - 0.178: 70 0.178 - 0.238: 1 0.238 - 0.297: 1 Chirality restraints: 2365 Sorted by residual: chirality pdb=" CA GLN C 276 " pdb=" N GLN C 276 " pdb=" C GLN C 276 " pdb=" CB GLN C 276 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA CYS B 786 " pdb=" N CYS B 786 " pdb=" C CYS B 786 " pdb=" CB CYS B 786 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CA CYS C 288 " pdb=" N CYS C 288 " pdb=" C CYS C 288 " pdb=" CB CYS C 288 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 2362 not shown) Planarity restraints: 4709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 622 " 0.046 2.00e-02 2.50e+03 8.26e-02 1.02e+02 pdb=" CG ASN A 622 " -0.096 2.00e-02 2.50e+03 pdb=" OD1 ASN A 622 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 622 " 0.140 2.00e-02 2.50e+03 pdb="HD21 ASN A 622 " 0.017 2.00e-02 2.50e+03 pdb="HD22 ASN A 622 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 668 " -0.041 2.00e-02 2.50e+03 4.84e-02 3.52e+01 pdb=" CD GLN A 668 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN A 668 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 668 " 0.071 2.00e-02 2.50e+03 pdb="HE21 GLN A 668 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 668 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 295 " -0.021 2.00e-02 2.50e+03 3.78e-02 2.15e+01 pdb=" CG ASN A 295 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 295 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 295 " -0.066 2.00e-02 2.50e+03 pdb="HD21 ASN A 295 " -0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 295 " 0.044 2.00e-02 2.50e+03 ... (remaining 4706 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 3058 2.22 - 2.81: 65440 2.81 - 3.41: 79486 3.41 - 4.00: 102587 4.00 - 4.60: 153751 Nonbonded interactions: 404322 Sorted by model distance: nonbonded pdb=" H GLN C 276 " pdb=" HA GLN C 276 " model vdw 1.624 1.816 nonbonded pdb=" H CYS C 288 " pdb=" HA CYS C 288 " model vdw 1.625 1.816 nonbonded pdb=" O HIS C 247 " pdb=" H CYS C 284 " model vdw 1.645 2.450 nonbonded pdb=" OD1 ASN C 255 " pdb=" H PHE C 258 " model vdw 1.657 2.450 nonbonded pdb=" O PRO C 432 " pdb=" H GLY C 463 " model vdw 1.660 2.450 ... (remaining 404317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB2 \ or name HB3 or name HD2 or name HE1 or name HE2)) or resid 2 through 266 or (re \ sid 267 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name H or name HA )) or (resid 268 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name \ H or name HA )) or resid 269 or (resid 270 through 271 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name H or name HA )) or resid 272 through 287 or (resid 288 \ and (name N or name CA or name C or name O or name CB or name SG or name H or n \ ame HA )) or resid 289 through 420 or (resid 421 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 422 through 691 or (resi \ d 692 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 693 through 719)) selection = (chain 'C' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA ) \ ) or (resid 14 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) \ or resid 15 through 369 or (resid 370 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 371 through 387 or (resid 388 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 389 through 624 or (resid 625 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 o \ r name H or name HA )) or resid 626 through 716 or (resid 717 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 718 through \ 719)) } ncs_group { reference = (chain 'B' and (resid 756 through 813 or (resid 814 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 815 through 914 or (r \ esid 915 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2 or name CD1 or name H or name HA )) or resid 916 or (resid 917 and (name \ N or name CA or name C or name CB or name CG or name CD or name CE or name NZ or \ name H or name HA )))) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 3 through 9 or (resid 10 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 11 th \ rough 20 or (resid 21 and (name N or name CA or name C or name CB or name CG or \ name OD1 or name ND2 or name H or name HA )))) selection = (chain 'G' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 3 through 21)) selection = (chain 'I' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 11 through 20 or (resid 21 \ and (name N or name CA or name C or name CB or name CG or name OD1 or name ND2 \ or name H or name HA )))) selection = (chain 'K' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 3 through 20 or (resid 21 and (name N \ or name CA or name C or name CB or name CG or name OD1 or name ND2 or name H or \ name HA )))) } ncs_group { reference = (chain 'F' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA )) or resid 2 \ 8 through 30)) selection = (chain 'H' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA )) or resid 2 \ 8 through 30)) selection = chain 'J' selection = (chain 'L' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA )) or resid 2 \ 8 through 30)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.006 0.060 16206 Z= 0.257 Angle : 0.972 13.327 22015 Z= 0.514 Chirality : 0.050 0.297 2365 Planarity : 0.007 0.107 2857 Dihedral : 14.587 89.574 5973 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.66 % Favored : 82.34 % Rotamer: Outliers : 0.62 % Allowed : 10.98 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -5.47 (0.15), residues: 1942 helix: -2.83 (0.24), residues: 257 sheet: -4.35 (0.28), residues: 177 loop : -4.06 (0.13), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG D 774 TYR 0.024 0.003 TYR K 14 PHE 0.017 0.003 PHE C 64 TRP 0.022 0.002 TRP A 183 HIS 0.022 0.003 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00578 (16157) covalent geometry : angle 0.93169 (21917) SS BOND : bond 0.00650 ( 49) SS BOND : angle 4.24737 ( 98) hydrogen bonds : bond 0.24493 ( 253) hydrogen bonds : angle 10.07322 ( 663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 522 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 511 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7767 (mpt-90) REVERT: A 49 LEU cc_start: 0.8498 (tp) cc_final: 0.8287 (mt) REVERT: A 96 PHE cc_start: 0.7854 (t80) cc_final: 0.7620 (t80) REVERT: A 120 GLU cc_start: 0.8377 (tt0) cc_final: 0.8080 (tt0) REVERT: A 123 ASN cc_start: 0.8574 (m-40) cc_final: 0.8236 (p0) REVERT: A 329 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8358 (mt-10) REVERT: A 355 GLU cc_start: 0.8855 (tt0) cc_final: 0.8337 (tp30) REVERT: B 869 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8489 (mm-30) REVERT: C 14 ARG cc_start: 0.6180 (ptp-170) cc_final: 0.5805 (mtm180) REVERT: C 123 ASN cc_start: 0.9030 (m110) cc_final: 0.8598 (t0) REVERT: C 245 TYR cc_start: 0.8445 (m-80) cc_final: 0.7864 (m-80) REVERT: C 373 SER cc_start: 0.9239 (m) cc_final: 0.8687 (p) REVERT: C 406 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7569 (mm110) REVERT: C 553 MET cc_start: 0.7550 (ptp) cc_final: 0.7261 (ptm) REVERT: C 575 GLU cc_start: 0.7180 (pm20) cc_final: 0.6654 (pm20) REVERT: C 609 SER cc_start: 0.8967 (p) cc_final: 0.8692 (t) REVERT: C 614 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8792 (mtpp) REVERT: D 781 ILE cc_start: 0.7622 (mp) cc_final: 0.7366 (mm) REVERT: F 18 VAL cc_start: 0.9057 (t) cc_final: 0.8777 (t) REVERT: J 3 ASN cc_start: 0.5014 (m110) cc_final: 0.4601 (p0) outliers start: 11 outliers final: 4 residues processed: 517 average time/residue: 0.3138 time to fit residues: 228.2046 Evaluate side-chains 377 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 373 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 78 ASN A 148 ASN A 189 GLN A 230 ASN A 247 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 298 ASN A 405 ASN A 406 GLN A 470 ASN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 HIS C 78 ASN C 100 HIS ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN C 589 GLN C 594 ASN C 668 GLN D 881 ASN D 894 ASN G 18 ASN E 5 GLN L 5 HIS J 3 ASN J 10 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.105272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090550 restraints weight = 190774.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.094268 restraints weight = 101720.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.096745 restraints weight = 61671.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.098394 restraints weight = 40984.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.099594 restraints weight = 29325.434| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16206 Z= 0.203 Angle : 0.755 9.245 22015 Z= 0.407 Chirality : 0.046 0.316 2365 Planarity : 0.007 0.096 2857 Dihedral : 8.130 62.717 2155 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.77 % Favored : 82.23 % Rotamer: Outliers : 0.28 % Allowed : 3.15 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -5.12 (0.15), residues: 1942 helix: -2.44 (0.26), residues: 265 sheet: -4.17 (0.29), residues: 187 loop : -3.82 (0.13), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 576 TYR 0.021 0.002 TYR C 430 PHE 0.025 0.002 PHE D 866 TRP 0.011 0.001 TRP A 183 HIS 0.020 0.002 HIS D 829 Details of bonding type rmsd covalent geometry : bond 0.00437 (16157) covalent geometry : angle 0.74104 (21917) SS BOND : bond 0.00700 ( 49) SS BOND : angle 2.27050 ( 98) hydrogen bonds : bond 0.06047 ( 253) hydrogen bonds : angle 8.56797 ( 663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 443 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8460 (pp) cc_final: 0.8251 (pp) REVERT: A 96 PHE cc_start: 0.7850 (t80) cc_final: 0.7613 (t80) REVERT: A 120 GLU cc_start: 0.8541 (tt0) cc_final: 0.8038 (tt0) REVERT: A 329 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8524 (mt-10) REVERT: A 355 GLU cc_start: 0.8833 (tt0) cc_final: 0.8292 (tp30) REVERT: A 419 LEU cc_start: 0.8991 (tt) cc_final: 0.8745 (tp) REVERT: A 507 TYR cc_start: 0.8900 (p90) cc_final: 0.8235 (p90) REVERT: A 692 ILE cc_start: 0.8740 (pt) cc_final: 0.8403 (pt) REVERT: B 779 TYR cc_start: 0.6894 (m-10) cc_final: 0.6661 (m-10) REVERT: C 12 ASP cc_start: 0.7316 (m-30) cc_final: 0.6766 (m-30) REVERT: C 110 MET cc_start: 0.5168 (mmt) cc_final: 0.4643 (mmt) REVERT: C 123 ASN cc_start: 0.8981 (m110) cc_final: 0.8465 (t0) REVERT: C 178 PHE cc_start: 0.8101 (m-80) cc_final: 0.7483 (m-80) REVERT: C 245 TYR cc_start: 0.8461 (m-80) cc_final: 0.7851 (m-80) REVERT: C 362 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7840 (mm-30) REVERT: C 371 ARG cc_start: 0.8093 (tpt-90) cc_final: 0.7607 (tpp80) REVERT: C 373 SER cc_start: 0.9206 (m) cc_final: 0.8405 (p) REVERT: C 403 LEU cc_start: 0.8835 (tp) cc_final: 0.8201 (tt) REVERT: C 404 ASP cc_start: 0.8808 (m-30) cc_final: 0.8266 (m-30) REVERT: C 453 GLU cc_start: 0.7849 (mp0) cc_final: 0.7644 (mp0) REVERT: C 533 ASP cc_start: 0.8562 (p0) cc_final: 0.8351 (p0) REVERT: C 553 MET cc_start: 0.7274 (ptp) cc_final: 0.7054 (ptm) REVERT: C 656 ARG cc_start: 0.8473 (mmp-170) cc_final: 0.8202 (mmp-170) REVERT: C 711 ASN cc_start: 0.8399 (t0) cc_final: 0.8129 (m-40) REVERT: E 4 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8717 (mt-10) outliers start: 5 outliers final: 0 residues processed: 445 average time/residue: 0.3051 time to fit residues: 192.4767 Evaluate side-chains 358 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 GLN C 34 GLN C 78 ASN C 100 HIS C 111 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN G 5 GLN H 10 HIS J 10 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.102707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.088021 restraints weight = 189055.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091673 restraints weight = 101090.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.094124 restraints weight = 61436.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.095742 restraints weight = 40917.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.096894 restraints weight = 29391.276| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16206 Z= 0.230 Angle : 0.762 9.627 22015 Z= 0.411 Chirality : 0.046 0.322 2365 Planarity : 0.006 0.091 2857 Dihedral : 8.174 61.494 2155 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.22 % 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: -4.89 (0.16), residues: 1942 helix: -2.05 (0.28), residues: 260 sheet: -4.16 (0.31), residues: 178 loop : -3.69 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 576 TYR 0.021 0.002 TYR K 14 PHE 0.023 0.002 PHE D 866 TRP 0.010 0.002 TRP A 251 HIS 0.020 0.002 HIS D 829 Details of bonding type rmsd covalent geometry : bond 0.00489 (16157) covalent geometry : angle 0.74608 (21917) SS BOND : bond 0.00628 ( 49) SS BOND : angle 2.45310 ( 98) hydrogen bonds : bond 0.05481 ( 253) hydrogen bonds : angle 8.15583 ( 663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 409 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 407 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.6948 (mt) cc_final: 0.6703 (mm) REVERT: A 36 LEU cc_start: 0.8560 (pp) cc_final: 0.8334 (pp) REVERT: A 120 GLU cc_start: 0.8391 (tt0) cc_final: 0.8074 (tt0) REVERT: A 278 VAL cc_start: 0.8927 (m) cc_final: 0.8625 (t) REVERT: A 329 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8473 (mt-10) REVERT: A 430 TYR cc_start: 0.8594 (m-80) cc_final: 0.8259 (m-80) REVERT: A 507 TYR cc_start: 0.8836 (p90) cc_final: 0.8375 (p90) REVERT: A 530 THR cc_start: 0.9123 (m) cc_final: 0.8877 (p) REVERT: A 574 ASP cc_start: 0.8115 (t0) cc_final: 0.7876 (t0) REVERT: A 692 ILE cc_start: 0.8821 (pt) cc_final: 0.8455 (pt) REVERT: B 779 TYR cc_start: 0.7027 (m-10) cc_final: 0.5699 (m-10) REVERT: C 123 ASN cc_start: 0.8680 (m110) cc_final: 0.8401 (t0) REVERT: C 245 TYR cc_start: 0.8454 (m-80) cc_final: 0.7844 (m-80) REVERT: C 362 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7802 (mm-30) REVERT: C 371 ARG cc_start: 0.8266 (tpt-90) cc_final: 0.7808 (tpp80) REVERT: C 373 SER cc_start: 0.9312 (m) cc_final: 0.8546 (p) REVERT: C 404 ASP cc_start: 0.8876 (m-30) cc_final: 0.8548 (m-30) REVERT: C 507 TYR cc_start: 0.9006 (p90) cc_final: 0.8795 (p90) REVERT: C 533 ASP cc_start: 0.8511 (p0) cc_final: 0.8282 (p0) REVERT: C 656 ARG cc_start: 0.8484 (mmp-170) cc_final: 0.8202 (mmp-170) REVERT: C 707 ASP cc_start: 0.8733 (m-30) cc_final: 0.8526 (m-30) REVERT: E 4 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8809 (mt-10) outliers start: 2 outliers final: 1 residues processed: 408 average time/residue: 0.3010 time to fit residues: 174.6136 Evaluate side-chains 341 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 340 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 96 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 140 optimal weight: 0.3980 chunk 186 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 622 ASN C 78 ASN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 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 = 0.3888 r_free = 0.3888 target = 0.104756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.089626 restraints weight = 187026.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.093431 restraints weight = 100717.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.095997 restraints weight = 61283.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.097705 restraints weight = 40585.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.098914 restraints weight = 28880.033| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16206 Z= 0.134 Angle : 0.660 8.683 22015 Z= 0.354 Chirality : 0.045 0.331 2365 Planarity : 0.005 0.088 2857 Dihedral : 7.651 62.959 2155 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.01 % Favored : 83.99 % Rotamer: Outliers : 0.11 % Allowed : 1.86 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.11 % 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: -4.56 (0.17), residues: 1942 helix: -1.58 (0.30), residues: 254 sheet: -3.96 (0.32), residues: 180 loop : -3.49 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 634 TYR 0.012 0.001 TYR C 512 PHE 0.017 0.002 PHE D 866 TRP 0.011 0.001 TRP A 183 HIS 0.011 0.001 HIS D 829 Details of bonding type rmsd covalent geometry : bond 0.00308 (16157) covalent geometry : angle 0.64698 (21917) SS BOND : bond 0.00449 ( 49) SS BOND : angle 2.05992 ( 98) hydrogen bonds : bond 0.04433 ( 253) hydrogen bonds : angle 7.66595 ( 663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8118 (mt0) cc_final: 0.7704 (mt0) REVERT: A 36 LEU cc_start: 0.8487 (pp) cc_final: 0.8182 (pp) REVERT: A 120 GLU cc_start: 0.8324 (tt0) cc_final: 0.7981 (tt0) REVERT: A 278 VAL cc_start: 0.8954 (m) cc_final: 0.8643 (t) REVERT: A 329 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8440 (mt-10) REVERT: A 355 GLU cc_start: 0.8784 (tt0) cc_final: 0.8297 (tp30) REVERT: A 430 TYR cc_start: 0.8525 (m-80) cc_final: 0.8234 (m-80) REVERT: A 505 LEU cc_start: 0.9151 (tp) cc_final: 0.8949 (tp) REVERT: A 507 TYR cc_start: 0.8871 (p90) cc_final: 0.8331 (p90) REVERT: A 574 ASP cc_start: 0.8173 (t0) cc_final: 0.7948 (t0) REVERT: A 692 ILE cc_start: 0.8835 (pt) cc_final: 0.8523 (pt) REVERT: A 709 LEU cc_start: 0.8191 (tt) cc_final: 0.7982 (tt) REVERT: C 86 ARG cc_start: 0.6971 (mpp80) cc_final: 0.6608 (mtt180) REVERT: C 123 ASN cc_start: 0.8667 (m110) cc_final: 0.8397 (t0) REVERT: C 245 TYR cc_start: 0.8414 (m-80) cc_final: 0.7775 (m-80) REVERT: C 362 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7895 (mm-30) REVERT: C 371 ARG cc_start: 0.8121 (tpt-90) cc_final: 0.7761 (tpp80) REVERT: C 372 ARG cc_start: 0.8265 (mtp180) cc_final: 0.8057 (mtp180) REVERT: C 373 SER cc_start: 0.9310 (m) cc_final: 0.8813 (p) REVERT: C 403 LEU cc_start: 0.8939 (tp) cc_final: 0.8212 (tt) REVERT: C 404 ASP cc_start: 0.8866 (m-30) cc_final: 0.8257 (m-30) REVERT: C 656 ARG cc_start: 0.8468 (mmp-170) cc_final: 0.8230 (mmp-170) REVERT: E 4 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8784 (mt-10) REVERT: J 3 ASN cc_start: 0.5071 (m-40) cc_final: 0.4687 (p0) outliers start: 2 outliers final: 0 residues processed: 409 average time/residue: 0.3080 time to fit residues: 178.8876 Evaluate side-chains 340 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 141 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 chunk 87 optimal weight: 4.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN C 21 HIS C 34 GLN C 78 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.104383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.089285 restraints weight = 185568.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.093086 restraints weight = 98861.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.095613 restraints weight = 59920.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.097306 restraints weight = 39726.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.098512 restraints weight = 28306.961| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16206 Z= 0.144 Angle : 0.641 11.998 22015 Z= 0.344 Chirality : 0.044 0.327 2365 Planarity : 0.005 0.088 2857 Dihedral : 7.468 63.634 2155 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.63 % Favored : 83.32 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.11 % 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: -4.40 (0.17), residues: 1942 helix: -1.27 (0.31), residues: 256 sheet: -3.75 (0.32), residues: 188 loop : -3.43 (0.14), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 389 TYR 0.013 0.001 TYR C 507 PHE 0.022 0.001 PHE C 96 TRP 0.011 0.001 TRP A 658 HIS 0.009 0.001 HIS D 829 Details of bonding type rmsd covalent geometry : bond 0.00324 (16157) covalent geometry : angle 0.63074 (21917) SS BOND : bond 0.00379 ( 49) SS BOND : angle 1.86216 ( 98) hydrogen bonds : bond 0.04277 ( 253) hydrogen bonds : angle 7.37725 ( 663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 409 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8026 (mt0) cc_final: 0.7669 (mt0) REVERT: A 36 LEU cc_start: 0.8434 (pp) cc_final: 0.8205 (pp) REVERT: A 120 GLU cc_start: 0.8301 (tt0) cc_final: 0.7830 (tt0) REVERT: A 278 VAL cc_start: 0.8866 (m) cc_final: 0.8543 (t) REVERT: A 329 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8518 (mt-10) REVERT: A 438 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8290 (tp30) REVERT: A 507 TYR cc_start: 0.8867 (p90) cc_final: 0.8318 (p90) REVERT: A 692 ILE cc_start: 0.8780 (pt) cc_final: 0.8464 (pt) REVERT: A 709 LEU cc_start: 0.8286 (tt) cc_final: 0.8081 (tt) REVERT: C 123 ASN cc_start: 0.8727 (m110) cc_final: 0.8403 (t0) REVERT: C 245 TYR cc_start: 0.8388 (m-80) cc_final: 0.7807 (m-80) REVERT: C 362 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7939 (mm-30) REVERT: C 371 ARG cc_start: 0.8159 (tpt-90) cc_final: 0.7816 (tpp80) REVERT: C 372 ARG cc_start: 0.8329 (mtp180) cc_final: 0.8099 (mtp180) REVERT: C 373 SER cc_start: 0.9308 (m) cc_final: 0.8806 (p) REVERT: C 404 ASP cc_start: 0.8795 (m-30) cc_final: 0.8515 (m-30) REVERT: C 553 MET cc_start: 0.7632 (ptp) cc_final: 0.7421 (ptm) REVERT: C 567 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8269 (tttt) REVERT: C 695 GLU cc_start: 0.8726 (mp0) cc_final: 0.8452 (mp0) REVERT: C 711 ASN cc_start: 0.8514 (t0) cc_final: 0.8002 (m110) REVERT: D 794 ARG cc_start: 0.8175 (ttt180) cc_final: 0.7568 (ttt90) REVERT: E 4 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8760 (mt-10) REVERT: J 3 ASN cc_start: 0.5248 (m-40) cc_final: 0.4909 (p0) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.3006 time to fit residues: 176.1043 Evaluate side-chains 339 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 55 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 168 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 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 = 0.3862 r_free = 0.3862 target = 0.103385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.088499 restraints weight = 183462.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.092243 restraints weight = 97790.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.094731 restraints weight = 59164.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096399 restraints weight = 39172.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.097588 restraints weight = 27886.562| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16206 Z= 0.154 Angle : 0.642 9.836 22015 Z= 0.344 Chirality : 0.044 0.326 2365 Planarity : 0.005 0.087 2857 Dihedral : 7.347 63.909 2155 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.48 % Favored : 83.52 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.16 % 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: -4.33 (0.17), residues: 1942 helix: -1.07 (0.32), residues: 246 sheet: -3.63 (0.31), residues: 199 loop : -3.39 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 576 TYR 0.013 0.001 TYR C 512 PHE 0.016 0.001 PHE A 258 TRP 0.012 0.001 TRP A 658 HIS 0.008 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00343 (16157) covalent geometry : angle 0.63298 (21917) SS BOND : bond 0.00346 ( 49) SS BOND : angle 1.73647 ( 98) hydrogen bonds : bond 0.04553 ( 253) hydrogen bonds : angle 7.34142 ( 663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8395 (pp) cc_final: 0.8174 (pp) REVERT: A 120 GLU cc_start: 0.8291 (tt0) cc_final: 0.7941 (tt0) REVERT: A 278 VAL cc_start: 0.8778 (m) cc_final: 0.8462 (t) REVERT: A 329 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8537 (mt-10) REVERT: A 353 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8645 (mt-10) REVERT: A 430 TYR cc_start: 0.8759 (m-10) cc_final: 0.8502 (m-80) REVERT: A 438 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8289 (tp30) REVERT: A 505 LEU cc_start: 0.9218 (tp) cc_final: 0.8992 (tp) REVERT: A 507 TYR cc_start: 0.8851 (p90) cc_final: 0.8287 (p90) REVERT: A 633 GLU cc_start: 0.8152 (pt0) cc_final: 0.7877 (pm20) REVERT: A 692 ILE cc_start: 0.8783 (pt) cc_final: 0.8518 (pt) REVERT: A 709 LEU cc_start: 0.8202 (tt) cc_final: 0.7997 (tt) REVERT: C 123 ASN cc_start: 0.8761 (m110) cc_final: 0.8418 (t0) REVERT: C 245 TYR cc_start: 0.8392 (m-80) cc_final: 0.7808 (m-80) REVERT: C 371 ARG cc_start: 0.8215 (tpt-90) cc_final: 0.7838 (tpp80) REVERT: C 373 SER cc_start: 0.9337 (m) cc_final: 0.8842 (p) REVERT: C 455 ASN cc_start: 0.8911 (p0) cc_final: 0.8594 (p0) REVERT: C 553 MET cc_start: 0.7703 (ptp) cc_final: 0.7430 (ptm) REVERT: C 567 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8249 (tttt) REVERT: C 656 ARG cc_start: 0.8535 (mmp-170) cc_final: 0.8317 (mmp-170) REVERT: C 695 GLU cc_start: 0.8723 (mp0) cc_final: 0.8453 (mp0) REVERT: C 707 ASP cc_start: 0.8761 (m-30) cc_final: 0.8507 (m-30) REVERT: E 4 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8770 (mt-10) REVERT: J 3 ASN cc_start: 0.5262 (m-40) cc_final: 0.4900 (p0) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.3064 time to fit residues: 172.9208 Evaluate side-chains 339 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 110 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN C 78 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.103134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.088217 restraints weight = 184870.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091955 restraints weight = 98217.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.094449 restraints weight = 59456.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.096122 restraints weight = 39340.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.097321 restraints weight = 28047.996| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16206 Z= 0.144 Angle : 0.632 8.440 22015 Z= 0.338 Chirality : 0.044 0.325 2365 Planarity : 0.005 0.087 2857 Dihedral : 7.212 64.816 2155 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.11 % 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: -4.25 (0.17), residues: 1942 helix: -1.01 (0.32), residues: 246 sheet: -3.61 (0.31), residues: 194 loop : -3.33 (0.14), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 576 TYR 0.016 0.001 TYR C 507 PHE 0.017 0.002 PHE A 572 TRP 0.013 0.001 TRP C 529 HIS 0.008 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00320 (16157) covalent geometry : angle 0.62383 (21917) SS BOND : bond 0.00376 ( 49) SS BOND : angle 1.64671 ( 98) hydrogen bonds : bond 0.04271 ( 253) hydrogen bonds : angle 7.24255 ( 663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 388 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8477 (pp) cc_final: 0.8234 (pp) REVERT: A 110 MET cc_start: 0.0789 (ttt) cc_final: 0.0358 (mmm) REVERT: A 120 GLU cc_start: 0.8307 (tt0) cc_final: 0.7965 (tt0) REVERT: A 278 VAL cc_start: 0.8762 (m) cc_final: 0.8442 (t) REVERT: A 329 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8462 (mt-10) REVERT: A 353 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8650 (mt-10) REVERT: A 355 GLU cc_start: 0.8894 (tt0) cc_final: 0.8451 (tp30) REVERT: A 405 ASN cc_start: 0.9276 (m-40) cc_final: 0.9068 (m-40) REVERT: A 430 TYR cc_start: 0.8745 (m-10) cc_final: 0.8472 (m-80) REVERT: A 438 GLU cc_start: 0.8805 (tp30) cc_final: 0.8565 (tp30) REVERT: A 505 LEU cc_start: 0.9208 (tp) cc_final: 0.8945 (tp) REVERT: A 507 TYR cc_start: 0.8844 (p90) cc_final: 0.8263 (p90) REVERT: A 633 GLU cc_start: 0.8064 (pt0) cc_final: 0.7768 (pm20) REVERT: A 692 ILE cc_start: 0.8802 (pt) cc_final: 0.8532 (pt) REVERT: A 709 LEU cc_start: 0.8159 (tt) cc_final: 0.7930 (tt) REVERT: C 88 PHE cc_start: 0.8787 (t80) cc_final: 0.8304 (t80) REVERT: C 123 ASN cc_start: 0.8830 (m110) cc_final: 0.8454 (t0) REVERT: C 245 TYR cc_start: 0.8395 (m-80) cc_final: 0.7757 (m-80) REVERT: C 371 ARG cc_start: 0.8215 (tpt-90) cc_final: 0.7862 (tpp80) REVERT: C 373 SER cc_start: 0.9343 (m) cc_final: 0.8825 (p) REVERT: C 455 ASN cc_start: 0.8898 (p0) cc_final: 0.8585 (p0) REVERT: C 656 ARG cc_start: 0.8572 (mmp-170) cc_final: 0.8352 (mmp-170) REVERT: C 695 GLU cc_start: 0.8731 (mp0) cc_final: 0.8455 (mp0) REVERT: C 707 ASP cc_start: 0.8727 (m-30) cc_final: 0.8515 (m-30) REVERT: G 14 TYR cc_start: 0.8011 (t80) cc_final: 0.7768 (t80) REVERT: E 4 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8784 (mt-10) REVERT: J 3 ASN cc_start: 0.5257 (m-40) cc_final: 0.4916 (p0) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.2989 time to fit residues: 167.1280 Evaluate side-chains 341 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 610 GLN C 32 HIS C 78 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 HIS J 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.100654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.086013 restraints weight = 188090.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089722 restraints weight = 99807.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.092169 restraints weight = 60162.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.093810 restraints weight = 39703.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.094984 restraints weight = 28255.137| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16206 Z= 0.200 Angle : 0.674 7.566 22015 Z= 0.363 Chirality : 0.044 0.321 2365 Planarity : 0.005 0.086 2857 Dihedral : 7.323 65.241 2155 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.62 % Favored : 80.38 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.05 % 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: -4.37 (0.17), residues: 1942 helix: -1.23 (0.31), residues: 246 sheet: -3.58 (0.32), residues: 195 loop : -3.41 (0.14), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 576 TYR 0.019 0.002 TYR A 646 PHE 0.026 0.002 PHE C 96 TRP 0.031 0.002 TRP C 529 HIS 0.012 0.002 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00434 (16157) covalent geometry : angle 0.66611 (21917) SS BOND : bond 0.00445 ( 49) SS BOND : angle 1.65409 ( 98) hydrogen bonds : bond 0.04598 ( 253) hydrogen bonds : angle 7.39957 ( 663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 382 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8467 (pp) cc_final: 0.8242 (pp) REVERT: A 110 MET cc_start: 0.0952 (ttt) cc_final: 0.0711 (mmm) REVERT: A 120 GLU cc_start: 0.8318 (tt0) cc_final: 0.7952 (tt0) REVERT: A 278 VAL cc_start: 0.8904 (m) cc_final: 0.8695 (t) REVERT: A 329 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8465 (mt-10) REVERT: A 353 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8712 (mt-10) REVERT: A 355 GLU cc_start: 0.8889 (tt0) cc_final: 0.8406 (tp30) REVERT: A 430 TYR cc_start: 0.8772 (m-10) cc_final: 0.8533 (m-80) REVERT: A 633 GLU cc_start: 0.8239 (pt0) cc_final: 0.7958 (pm20) REVERT: A 692 ILE cc_start: 0.8827 (pt) cc_final: 0.8576 (pt) REVERT: A 709 LEU cc_start: 0.8282 (tt) cc_final: 0.8060 (tt) REVERT: C 88 PHE cc_start: 0.8833 (t80) cc_final: 0.8470 (t80) REVERT: C 110 MET cc_start: 0.5144 (mmt) cc_final: 0.4745 (mmt) REVERT: C 123 ASN cc_start: 0.8925 (m110) cc_final: 0.8496 (t0) REVERT: C 245 TYR cc_start: 0.8405 (m-80) cc_final: 0.7823 (m-80) REVERT: C 371 ARG cc_start: 0.8380 (tpt-90) cc_final: 0.7995 (tpp80) REVERT: C 373 SER cc_start: 0.9338 (m) cc_final: 0.8832 (p) REVERT: C 656 ARG cc_start: 0.8602 (mmp-170) cc_final: 0.8395 (mmp-170) REVERT: C 695 GLU cc_start: 0.8779 (mp0) cc_final: 0.8489 (mp0) REVERT: C 707 ASP cc_start: 0.8743 (m-30) cc_final: 0.8479 (m-30) REVERT: C 711 ASN cc_start: 0.8605 (t0) cc_final: 0.8297 (m110) REVERT: E 4 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8798 (mt-10) REVERT: J 3 ASN cc_start: 0.5305 (m-40) cc_final: 0.4993 (p0) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.2931 time to fit residues: 159.1749 Evaluate side-chains 339 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 16 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.101582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.086895 restraints weight = 186888.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.090658 restraints weight = 99257.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.093120 restraints weight = 59648.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.094772 restraints weight = 39379.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095941 restraints weight = 27924.252| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16206 Z= 0.159 Angle : 0.641 6.650 22015 Z= 0.343 Chirality : 0.044 0.325 2365 Planarity : 0.005 0.086 2857 Dihedral : 7.252 66.471 2155 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.25 % Favored : 82.75 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -4.28 (0.17), residues: 1942 helix: -1.13 (0.31), residues: 246 sheet: -3.53 (0.31), residues: 195 loop : -3.36 (0.14), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 389 TYR 0.020 0.002 TYR C 507 PHE 0.021 0.002 PHE D 866 TRP 0.021 0.001 TRP C 529 HIS 0.012 0.001 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00350 (16157) covalent geometry : angle 0.63324 (21917) SS BOND : bond 0.00432 ( 49) SS BOND : angle 1.61208 ( 98) hydrogen bonds : bond 0.04395 ( 253) hydrogen bonds : angle 7.26751 ( 663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6699 (mtt180) REVERT: A 36 LEU cc_start: 0.8413 (pp) cc_final: 0.8159 (pp) REVERT: A 110 MET cc_start: 0.1245 (ttt) cc_final: 0.1019 (mmm) REVERT: A 120 GLU cc_start: 0.8278 (tt0) cc_final: 0.7936 (tt0) REVERT: A 278 VAL cc_start: 0.8883 (m) cc_final: 0.8475 (t) REVERT: A 329 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8412 (mt-10) REVERT: A 353 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8697 (mt-10) REVERT: A 355 GLU cc_start: 0.8850 (tt0) cc_final: 0.8425 (tp30) REVERT: A 430 TYR cc_start: 0.8750 (m-10) cc_final: 0.8515 (m-80) REVERT: A 633 GLU cc_start: 0.8214 (pt0) cc_final: 0.7875 (pm20) REVERT: A 692 ILE cc_start: 0.8827 (pt) cc_final: 0.8589 (pt) REVERT: A 709 LEU cc_start: 0.8186 (tt) cc_final: 0.7932 (tt) REVERT: C 88 PHE cc_start: 0.8839 (t80) cc_final: 0.8422 (t80) REVERT: C 110 MET cc_start: 0.4988 (mmt) cc_final: 0.4721 (mmt) REVERT: C 123 ASN cc_start: 0.8944 (m110) cc_final: 0.8502 (t0) REVERT: C 178 PHE cc_start: 0.8258 (m-80) cc_final: 0.7648 (m-80) REVERT: C 245 TYR cc_start: 0.8369 (m-80) cc_final: 0.7775 (m-80) REVERT: C 371 ARG cc_start: 0.8328 (tpt-90) cc_final: 0.7972 (tpp80) REVERT: C 373 SER cc_start: 0.9331 (m) cc_final: 0.8836 (p) REVERT: C 656 ARG cc_start: 0.8597 (mmp-170) cc_final: 0.8373 (mmp-170) REVERT: C 695 GLU cc_start: 0.8768 (mp0) cc_final: 0.8470 (mp0) REVERT: C 707 ASP cc_start: 0.8726 (m-30) cc_final: 0.8482 (m-30) REVERT: C 711 ASN cc_start: 0.8592 (t0) cc_final: 0.8339 (m110) REVERT: G 14 TYR cc_start: 0.8041 (t80) cc_final: 0.7798 (t80) REVERT: E 4 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8767 (mt-10) REVERT: J 3 ASN cc_start: 0.5334 (m-40) cc_final: 0.5027 (p0) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.3002 time to fit residues: 167.8184 Evaluate side-chains 343 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 138 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 161 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.102723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.088064 restraints weight = 186929.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091809 restraints weight = 99225.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.094265 restraints weight = 59799.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.095906 restraints weight = 39554.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097075 restraints weight = 28176.384| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16206 Z= 0.139 Angle : 0.645 7.791 22015 Z= 0.342 Chirality : 0.045 0.345 2365 Planarity : 0.005 0.086 2857 Dihedral : 7.156 67.541 2155 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.77 % Favored : 82.23 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.05 % 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: -4.24 (0.17), residues: 1942 helix: -1.08 (0.31), residues: 252 sheet: -3.51 (0.31), residues: 200 loop : -3.32 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 389 TYR 0.019 0.001 TYR C 507 PHE 0.049 0.002 PHE A 76 TRP 0.016 0.001 TRP C 529 HIS 0.012 0.001 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00313 (16157) covalent geometry : angle 0.63329 (21917) SS BOND : bond 0.00527 ( 49) SS BOND : angle 1.91571 ( 98) hydrogen bonds : bond 0.04151 ( 253) hydrogen bonds : angle 7.17745 ( 663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue ILE 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue ILE 82 is missing expected H atoms. Skipping. Residue ILE 95 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ILE 119 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ILE 158 is missing expected H atoms. Skipping. Residue ILE 174 is missing expected H atoms. Skipping. Residue ILE 195 is missing expected H atoms. Skipping. Residue LYS 267 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue ILE 285 is missing expected H atoms. Skipping. Residue ILE 321 is missing expected H atoms. Skipping. Residue ILE 336 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 344 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ILE 370 is missing expected H atoms. Skipping. Residue ILE 388 is missing expected H atoms. Skipping. Residue ILE 395 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue ILE 439 is missing expected H atoms. Skipping. Residue ILE 457 is missing expected H atoms. Skipping. Residue ILE 478 is missing expected H atoms. Skipping. Residue ILE 485 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue ILE 564 is missing expected H atoms. Skipping. Residue ILE 585 is missing expected H atoms. Skipping. Residue ILE 586 is missing expected H atoms. Skipping. Residue ILE 602 is missing expected H atoms. Skipping. Residue ILE 611 is missing expected H atoms. Skipping. Residue ILE 612 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 692 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue ILE 814 is missing expected H atoms. Skipping. Residue ILE 822 is missing expected H atoms. Skipping. Residue ILE 842 is missing expected H atoms. Skipping. Residue ILE 886 is missing expected H atoms. Skipping. Residue ILE 915 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASN G 21 " (corrupted residue). Skipping it. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Evaluate side-chains 387 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS D 917 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6921 (mtt180) cc_final: 0.6586 (mtt180) REVERT: A 36 LEU cc_start: 0.8502 (pp) cc_final: 0.8231 (pp) REVERT: A 120 GLU cc_start: 0.8272 (tt0) cc_final: 0.7914 (tt0) REVERT: A 278 VAL cc_start: 0.8859 (m) cc_final: 0.8540 (t) REVERT: A 324 VAL cc_start: 0.9305 (p) cc_final: 0.8961 (p) REVERT: A 329 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8424 (mt-10) REVERT: A 355 GLU cc_start: 0.8860 (tt0) cc_final: 0.8404 (tp30) REVERT: A 430 TYR cc_start: 0.8755 (m-10) cc_final: 0.8506 (m-80) REVERT: A 633 GLU cc_start: 0.8066 (pt0) cc_final: 0.7743 (pm20) REVERT: A 695 GLU cc_start: 0.8223 (mp0) cc_final: 0.8017 (mp0) REVERT: A 709 LEU cc_start: 0.8268 (tt) cc_final: 0.8031 (tt) REVERT: C 88 PHE cc_start: 0.8825 (t80) cc_final: 0.8405 (t80) REVERT: C 123 ASN cc_start: 0.8972 (m110) cc_final: 0.8498 (t0) REVERT: C 178 PHE cc_start: 0.8236 (m-80) cc_final: 0.7609 (m-80) REVERT: C 245 TYR cc_start: 0.8360 (m-80) cc_final: 0.7773 (m-80) REVERT: C 371 ARG cc_start: 0.8262 (tpt-90) cc_final: 0.7926 (tpp80) REVERT: C 373 SER cc_start: 0.9344 (m) cc_final: 0.8826 (p) REVERT: C 656 ARG cc_start: 0.8617 (mmp-170) cc_final: 0.8414 (mmp-170) REVERT: C 695 GLU cc_start: 0.8769 (mp0) cc_final: 0.8461 (mp0) REVERT: C 711 ASN cc_start: 0.8486 (t0) cc_final: 0.8263 (m110) REVERT: G 14 TYR cc_start: 0.8116 (t80) cc_final: 0.7882 (t80) REVERT: E 4 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8749 (mt-10) REVERT: J 3 ASN cc_start: 0.5236 (m-40) cc_final: 0.4974 (p0) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.3004 time to fit residues: 166.9480 Evaluate side-chains 347 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 193 optimal weight: 0.0570 chunk 164 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN C 15 ASN C 78 ASN C 280 HIS C 295 ASN ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.103543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.088731 restraints weight = 185667.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.092532 restraints weight = 98751.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.095031 restraints weight = 59588.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.096710 restraints weight = 39291.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.097908 restraints weight = 27898.666| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16206 Z= 0.118 Angle : 0.611 6.854 22015 Z= 0.325 Chirality : 0.044 0.334 2365 Planarity : 0.005 0.086 2857 Dihedral : 6.960 68.776 2155 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.55 % Favored : 84.45 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.05 % 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: -4.08 (0.17), residues: 1942 helix: -0.84 (0.31), residues: 253 sheet: -3.39 (0.31), residues: 198 loop : -3.24 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 389 TYR 0.015 0.001 TYR C 507 PHE 0.037 0.001 PHE A 76 TRP 0.015 0.001 TRP C 529 HIS 0.009 0.001 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00274 (16157) covalent geometry : angle 0.60193 (21917) SS BOND : bond 0.00466 ( 49) SS BOND : angle 1.71387 ( 98) hydrogen bonds : bond 0.03977 ( 253) hydrogen bonds : angle 7.07099 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5161.43 seconds wall clock time: 88 minutes 59.57 seconds (5339.57 seconds total)